Hi There,
I am using the command below to download raw fastq files from BioProject accession: PRJNA354235 for metagenomic and metatranscriptomic research.
esearch -db sra -query PRJNA354235 | efetch --format runinfo | cut -d ',' -f 1| grep SRR |xargs fastq-dump --split-file
The command works just fine at first then suddenly at SRR6451769 the process stops and prints ncbi_error_report.txt. Is there a way to get around this or for the command to ignore an error and continue trying to move forward? The error report is below.
Thank you for your time!
<Report>
<Run>
<Date>
<Start value="Fri Jan 3 2020 6:30:55 PM"/>
<End value="Fri Jan 3 2020 6:33:13 PM"/>
</Date>
<Home name="HOME" value="/home/ubuntu"/>
<Cwd>/home/ubuntu/data2</Cwd>
<CommandLine argc="2">
<Arg index="0" value="/usr/local/ncbi/sra-tools/bin/fastq-dump"/>
<Arg index="1" value="SRR6451769"/>
</CommandLine>
<Result rc="RC(rcPS,rcCondition,rcWaiting,rcTimeout,rcExhausted)"/>
<User admin="false"/>
</Run>
<Configuration>
<Files count="3">
<File name="/etc/ncbi/certs.kfg"/>
<File name="/etc/ncbi/default.kfg"/>
<File name="/etc/ncbi/vdb-copy.kfg"/>
</Files>
<refseq state="not found"/>
<krypto state="pwfile: not found"/>
<sra state="not found"/>
<Config>
<ConfigurationFiles>
/etc/ncbi/certs.kfg
/etc/ncbi/default.kfg
/etc/ncbi/vdb-copy.kfg
</ConfigurationFiles>
<APPNAME>"fastq-dump"</APPNAME>
<APPPATH>"/usr/local/ncbi/sra-tools/bin"</APPPATH>
<AWS></AWS>
<BUILD>"RELEASE"</BUILD>
<HOME>"/home/ubuntu"</HOME>
<HOST></HOST>
<NCBI_HOME>"/home/ubuntu/.ncbi"</NCBI_HOME>
<NCBI_SETTINGS>"/home/ubuntu/.ncbi/user-settings.mkfg"</NCBI_SETTINGS>
<OS>"linux"</OS>
<PWD>"/home/ubuntu/data2"</PWD>
<USER>"ubuntu"</USER>
<VDBCOPY>
<DO_NOT_REDACT>"CS_KEY,FLOW_CHARS,KEY_SEQUENCE,LINKER_SEQUENCE"</DO_NOT_REDACT>
<META>
<IGNORE>"col,.seq,STATS,BASE_COUNT,HUFFMAN_TREE_POS,HUFFMAN_TREE_POS_SIZE,HUFFMAN_TREE_PRB,HUFFMAN_TREE_PRB_SIZE,HUFFMAN_TREE_SIG,HUFFMAN_TREE_SIG_SIZE,MSC454_CLIP_QUALITY_LEFT,MSC454_CLIP_QUALITY_RIGHT,MSC454_FLOW_CHARS,MSC454_KEY_SEQUENCE,NREADS,NUMBER_POS_CHANNELS,NUMBER_PRB_CHANNELS_1,NUMBER_PRB_COLUMNS,NUMBER_SIG_CHANNELS,PLATFORM,READ_0,READ_1,SPOT_COUNT"</IGNORE>
</META>
<NCBI_SRA_ABI_tbl_v1_1>
<schema>"sra/abi.vschema"</schema>
<tab>"NCBI:SRA:ABI:tbl:v2"</tab>
</NCBI_SRA_ABI_tbl_v1_1>
<NCBI_SRA_Illumina_tbl_v0a_1>
<schema>"sra/illumina.vschema"</schema>
<tab>"NCBI:SRA:Illumina:tbl:phred:v2"</tab>
</NCBI_SRA_Illumina_tbl_v0a_1>
<NCBI_SRA__454__tbl_v0_1>
<schema>"sra/454.vschema"</schema>
<tab>"NCBI:SRA:_454_:tbl:v2"</tab>
</NCBI_SRA__454__tbl_v0_1>
<READ_FILTER_COL_NAME>"READ_FILTER"</READ_FILTER_COL_NAME>
<REDACTABLE_TYPES>"INSDC:color:text,INSDC:x2cs:bin,INSDC:2cs:bin,INSDC:2cs:packed,INSDC:dna:text,INSDC:4na:bin,INSDC:4na:packed,INSDC:x2na:bin,INSDC:2na:bin,INSDC:2na:packed,NCBI:SRA:pos16,INSDC:quality:phred,INSDC:quality:log_odds,NCBI:qual4,INSDC:position:one,INSDC:position:zero,NCBI:fsamp4,NCBI:isamp1"</REDACTABLE_TYPES>
<REDACTVALUE>
<INSDC_color_text>
<VALUE>"'.'"</VALUE>
</INSDC_color_text>
<INSDC_dna_text>
<VALUE>"'N'"</VALUE>
</INSDC_dna_text>
<NCBI_qual4>
<VALUE>"-6"</VALUE>
</NCBI_qual4>
<TYPES>"INSDC_color_text,INSDC_dna_text,NCBI_qual4"</TYPES>
</REDACTVALUE>
<SCORE>
<INSDC_2cs_bin>"2"</INSDC_2cs_bin>
<INSDC_2cs_packed>"2"</INSDC_2cs_packed>
<INSDC_2na_bin>"2"</INSDC_2na_bin>
<INSDC_2na_packed>"2"</INSDC_2na_packed>
<INSDC_SRA_read_type>"1"</INSDC_SRA_read_type>
<INSDC_quality_log_odds>"1"</INSDC_quality_log_odds>
<INSDC_quality_phred>"1"</INSDC_quality_phred>
<INSDC_x2cs_bin>"1"</INSDC_x2cs_bin>
<INSDC_x2na_bin>"1"</INSDC_x2na_bin>
</SCORE>
<_454_>
<schema>"sra/454.vschema"</schema>
<tab>"NCBI:SRA:_454_:tbl:v2"</tab>
<_ABSOLID_>
<schema>"sra/abi.vschema"</schema>
<tab>"NCBI:SRA:ABI:tbl:v2"</tab>
<_ILLUMINA_>
<schema>"sra/illumina.vschema"</schema>
<tab>"NCBI:SRA:Illumina:tbl:phred:v2"</tab>
</VDBCOPY>
<VDB_CONFIG></VDB_CONFIG>
<VDB_ROOT></VDB_ROOT>
<config>
<default>"true"</default>
</config>
<kfg>
<arch>
<bits>"64"</bits>
<name>"ip-172-31-89-243"</name>
</arch>
"/etc/ncbi"
<name>"default.kfg"</name>
</kfg>
<repository>
<remote>
<main>
<CGI>
<resolver-cgi>"https://trace.ncbi.nlm.nih.gov/Traces/names/names.fcgi"</resolver-cgi>
</CGI>
<SDL.2>
<resolver-cgi>"https://trace.ncbi.nlm.nih.gov/Traces/sdl/2/retrieve"</resolver-cgi>
</SDL.2>
</main>
<protected>
<CGI>
<resolver-cgi>"https://trace.ncbi.nlm.nih.gov/Traces/names/names.fcgi"</resolver-cgi>
</CGI>
</protected>
</remote>
<user>
<ad>
<public>
<apps>
<file>
<volumes>
<flat>"."</flat>
</volumes>
</file>
<refseq>
<volumes>
<refseqAd>"."</refseqAd>
</volumes>
</refseq>
<sra>
<volumes>
<sraAd>"."</sraAd>
</volumes>
</sra>
<sraPileup>
<volumes>
<ad>"."</ad>
</volumes>
</sraPileup>
<sraRealign>
<volumes>
<ad>"."</ad>
</volumes>
</sraRealign>
</apps>
<root>"."</root>
</public>
</ad>
<main>
<public>
<apps>
<file>
<volumes>
<flat>"files"</flat>
</volumes>
</file>
<nakmer>
<volumes>
<nakmerFlat>"nannot"</nakmerFlat>
</volumes>
</nakmer>
<nannot>
<volumes>
<nannotFlat>"nannot"</nannotFlat>
</volumes>
</nannot>
<refseq>
<volumes>
<refseq>"refseq"</refseq>
</volumes>
</refseq>
<sra>
<volumes>
<sraFlat>"sra"</sraFlat>
</volumes>
</sra>
<sraPileup>
<volumes>
<flat>"sra"</flat>
</volumes>
</sraPileup>
<sraRealign>
<volumes>
<flat>"sra"</flat>
</volumes>
</sraRealign>
<wgs>
<volumes>
<wgsFlat>"wgs"</wgsFlat>
</volumes>
</wgs>
</apps>
</public>
</main>
</user>
</repository>
<tls>
<ca.crt>
<ncbi1>"-----BEGIN CERTIFICATE-----\x0D\x0AMIIDrzCCApegAwIBAgIQCDvgVpBCRrGhdWrJWZHHSjANBgkqhkiG9w0BAQUFADBh\x0D\x0AMQswCQYDVQQGEwJVUzEVMBMGA1UEChMMRGlnaUNlcnQgSW5jMRkwFwYDVQQLExB3\x0D\x0Ad3cuZGlnaWNlcnQuY29tMSAwHgYDVQQDExdEaWdpQ2VydCBHbG9iYWwgUm9vdCBD\x0D\x0AQTAeFw0wNjExMTAwMDAwMDBaFw0zMTExMTAwMDAwMDBaMGExCzAJBgNVBAYTAlVT\x0D\x0AMRUwEwYDVQQKEwxEaWdpQ2VydCBJbmMxGTAXBgNVBAsTEHd3dy5kaWdpY2VydC5j\x0D\x0Ab20xIDAeBgNVBAMTF0RpZ2lDZXJ0IEdsb2JhbCBSb290IENBMIIBIjANBgkqhkiG\x0D\x0A9w0BAQEFAAOCAQ8AMIIBCgKCAQEA4jvhEXLeqKTTo1eqUKKPC3eQyaKl7hLOllsB\x0D\x0ACSDMAZOnTjC3U/dDxGkAV53ijSLdhwZAAIEJzs4bg7/fzTtxRuLWZscFs3YnFo97\x0D\x0Anh6Vfe63SKMI2tavegw5BmV/Sl0fvBf4q77uKNd0f3p4mVmFaG5cIzJLv07A6Fpt\x0D\x0A43C/dxC//AH2hdmoRBBYMql1GNXRor5H4idq9Joz+EkIYIvUX7Q6hL+hqkpMfT7P\x0D\x0AT19sdl6gSzeRntwi5m3OFBqOasv+zbMUZBfHWymeMr/y7vrTC0LUq7dBMtoM1O/4\x0D\x0AgdW7jVg/tRvoSSiicNoxBN33shbyTApOB6jtSj1etX+jkMOvJwIDAQABo2MwYTAO\x0D\x0ABgNVHQ8BAf8EBAMCAYYwDwYDVR0TAQH/BAUwAwEB/zAdBgNVHQ4EFgQUA95QNVbR\x0D\x0ATLtm8KPiGxvDl7I90VUwHwYDVR0jBBgwFoAUA95QNVbRTLtm8KPiGxvDl7I90VUw\x0D\x0ADQYJKoZIhvcNAQEFBQADggEBAMucN6pIExIK+t1EnE9SsPTfrgT1eXkIoyQY/Esr\x0D\x0AhMAtudXH/vTBH1jLuG2cenTnmCmrEbXjcKChzUyImZOMkXDiqw8cvpOp/2PV5Adg\x0D\x0A06O/nVsJ8dWO41P0jmP6P6fbtGbfYmbW0W5BjfIttep3Sp+dWOIrWcBAI+0tKIJF\x0D\x0APnlUkiaY4IBIqDfv8NZ5YBberOgOzW6sRBc4L0na4UU+Krk2U886UAb3LujEV0ls\x0D\x0AYSEY1QSteDwsOoBrp+uvFRTp2InBuThs4pFsiv9kuXclVzDAGySj4dzp30d8tbQk\x0D\x0ACAUw7C29C79Fv1C5qfPrmAESrciIxpg0X40KPMbp1ZWVbd4wOTAeBggrBgEFBQcD\x0D\x0ABAYIKwYBBQUHAwEGCCsGAQUFBwMDDBdEaWdpQ2VydCBHbG9iYWwgUm9vdCBDQQ==\x0D\x0A-----END CERTIFICATE-----\x0D\x0A"</ncbi1>
<ncbi2>"-----BEGIN CERTIFICATE-----\x0D\x0AMIIDxTCCAq2gAwIBAgIQAqxcJmoLQJuPC3nyrkYldzANBgkqhkiG9w0BAQUFADBs\x0D\x0AMQswCQYDVQQGEwJVUzEVMBMGA1UEChMMRGlnaUNlcnQgSW5jMRkwFwYDVQQLExB3\x0D\x0Ad3cuZGlnaWNlcnQuY29tMSswKQYDVQQDEyJEaWdpQ2VydCBIaWdoIEFzc3VyYW5j\x0D\x0AZSBFViBSb290IENBMB4XDTA2MTExMDAwMDAwMFoXDTMxMTExMDAwMDAwMFowbDEL\x0D\x0AMAkGA1UEBhMCVVMxFTATBgNVBAoTDERpZ2lDZXJ0IEluYzEZMBcGA1UECxMQd3d3\x0D\x0ALmRpZ2ljZXJ0LmNvbTErMCkGA1UEAxMiRGlnaUNlcnQgSGlnaCBBc3N1cmFuY2Ug\x0D\x0ARVYgUm9vdCBDQTCCASIwDQYJKoZIhvcNAQEBBQADggEPADCCAQoCggEBAMbM5XPm\x0D\x0A+9S75S0tMqbf5YE/yc0lSbZxKsPVlDRnogocsF9ppkCxxLeyj9CYpKlBWTrT3JTW\x0D\x0APNt0OKRKzE0lgvdKpVMSOO7zSW1xkX5jtqumX8OkhPhPYlG++MXs2ziS4wblCJEM\x0D\x0AxChBVfvLWokVfnHoNb9Ncgk9vjo4UFt3MRuNs8ckRZqnrG0AFFoEt7oT61EKmEFB\x0D\x0AIk5lYYeBQVCmeVyJ3hlKV9Uu5l0cUyx+mM0aBhakaHPQNAQTXKFx01p8VdteZOE3\x0D\x0AhzBWBOURtCmAEvF5OYiiAhF8J2a3iLd48soKqDirCmTCv2ZdlYTBoSUeh10aUAsg\x0D\x0AEsxBu24LUTi4S8sCAwEAAaNjMGEwDgYDVR0PAQH/BAQDAgGGMA8GA1UdEwEB/wQF\x0D\x0AMAMBAf8wHQYDVR0OBBYEFLE+w2kD+L9HAdSYJhoIAu9jZCvDMB8GA1UdIwQYMBaA\x0D\x0AFLE+w2kD+L9HAdSYJhoIAu9jZCvDMA0GCSqGSIb3DQEBBQUAA4IBAQAcGgaX3Nec\x0D\x0AnzyIZgYIVyHbIUf4KmeqvxgydkAQV8GK83rZEWWONfqe/EW1ntlMMUu4kehDLI6z\x0D\x0AeM7b41N5cdblIZQB2lWHmiRk9opmzN6cN82oNLFpmyPInngiK3BD41VHMWEZ71jF\x0D\x0AhS9OMPagMRYjyOfiZRYzy78aG6A9+MpeizGLYAiJLQwGXFK3xPkKmNEVX58Svnw2\x0D\x0AYzi9RKR/5CYrCsSXaQ3pjOLAEFe4yHYSkVXySGnYvCoCWw9E1CAx2/S6cCZdkGCe\x0D\x0AvEsXCS+0yx5DaMkHJ8HSXPfqIbloEpw8nL+e/IBcm2PN7EeqJSdnoDfzAIJ9VNep\x0D\x0A+OkuE6N36B9KMEQwHgYIKwYBBQUHAwQGCCsGAQUFBwMBBggrBgEFBQcDAwwiRGln\x0D\x0AaUNlcnQgSGlnaCBBc3N1cmFuY2UgRVYgUm9vdCBDQQ==\x0D\x0A-----END CERTIFICATE-----\x0D\x0A"</ncbi2>
</ca.crt>
</tls>
<tools>
<ascp>
<max_rate>"450m"</max_rate>
</ascp>
</tools>
<vdb>
<lib>
<paths>
<kfg>"/usr/local/ncbi/sra-tools/bin"</kfg>
</paths>
</lib>
</vdb>
</Config>
<RemoteAccess available="true"/>
<CurrentProtectedRepository found="false"/>
</Configuration>
<Object path="SRR6451769" type="table" fs_type="unexpected">
</Object>
<SOFTWARE>
<VDBLibrary vers="2.7.32"/>
<Build static="true">
<Module name=""/>
</Build>
<Tool date="Aug 13 2019" name="/usr/local/ncbi/sra-tools/bin/fastq-dump" vers="2.10">
<Binary path="/usr/local/ncbi/sra-tools/bin/fastq-dump" type="alias" md5="ae4edbb7ad442f57834b3b7f7596f30d">
<Alias resolved="fastq-dump.2">
<Alias resolved="fastq-dump.2.10.0">
<Alias resolved="sratools.2.10.0"/>
</Alias>
</Alias>
</Binary>
</Tool>
</SOFTWARE>
<Env>
</Env>
</Report>
This does not look like an error report even though it may be saved in a file with error in its name. There are 2598 samples in this set. How many are you able to successfully recover before you run into a problem.