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5 days ago
ongchip
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(base) ongchip@ongchip-LINUX:~/ongchip-DP/work/202408$ $TRINITY_HOME/Trinity --seqType fq --max_memory 10G --left A1_1_paired.fq.gz --right A1_2_paired.fq.gz --CPU 2
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Trinity-v2.15.2
Left read files: $VAR1 = [
'A1_1_paired.fq.gz'
];
Right read files: $VAR1 = [
'A1_2_paired.fq.gz'
];
Trinity version: Trinity-v2.15.2
-currently using the latest production release of Trinity.
Tuesday, October 29, 2024: 16:45:19 CMD: java -Xmx64m -XX:ParallelGCThreads=2 -jar /usr/local/bin/util/support_scripts/ExitTester.jar 0
Tuesday, October 29, 2024: 16:45:19 CMD: java -Xmx4g -XX:ParallelGCThreads=2 -jar /usr/local/bin/util/support_scripts/ExitTester.jar 1
----------------------------------------------------------------------------------
-------------- Trinity Phase 1: Clustering of RNA-Seq Reads ---------------------
----------------------------------------------------------------------------------
---------------------------------------------------------------
------------ In silico Read Normalization ---------------------
-- (Removing Excess Reads Beyond 200 Coverage --
---------------------------------------------------------------
# running normalization on reads: $VAR1 = [
[
'/home/ongchip/ongchip-DP/work/202408/A1_1_paired.fq.gz'
],
[
'/home/ongchip/ongchip-DP/work/202408/A1_2_paired.fq.gz'
]
];
Tuesday, October 29, 2024: 16:45:19 CMD: /usr/local/bin/util/insilico_read_normalization.pl --seqType fq --JM 10G --max_cov 200 --min_cov 1 --CPU 2 --output /home/ongchip/ongchip-DP/work/202408/trinity_out_dir/insilico_read_normalization --max_CV 10000 --left /home/ongchip/ongchip-DP/work/202408/A1_1_paired.fq.gz --right /home/ongchip/ongchip-DP/work/202408/A1_2_paired.fq.gz --pairs_together --PARALLEL_STATS
-prepping seqs
Converting input files. (both directions in parallel);CMD: seqtk-trinity seq -A -R 1 <(gunzip -c /home/ongchip/ongchip-DP/work/202408/A1_1_paired.fq.gz) >> left.fa
CMD: seqtk-trinity seq -A -R 2 <(gunzip -c /home/ongchip/ongchip-DP/work/202408/A1_2_paired.fq.gz) >> right.fa
CMD finished (328 seconds)
CMD finished (328 seconds)
CMD: touch left.fa.ok
CMD finished (1 seconds)
CMD: touch right.fa.ok
CMD finished (1 seconds)
Done converting input files. CMD: cat left.fa right.fa > both.fa
CMD finished (139 seconds)
CMD: touch both.fa.ok
CMD finished (0 seconds)
-kmer counting.
-------------------------------------------
----------- Jellyfish --------------------
-- (building a k-mer catalog from reads) --
-------------------------------------------
CMD: jellyfish count -t 2 -m 25 -s 100000000 --canonical both.fa
CMD finished (701 seconds)
CMD: jellyfish histo -t 2 -o jellyfish.K25.min2.kmers.fa.histo mer_counts.jf
CMD finished (23 seconds)
CMD: jellyfish dump -L 2 mer_counts.jf > jellyfish.K25.min2.kmers.fa
CMD finished (61 seconds)
CMD: touch jellyfish.K25.min2.kmers.fa.success
CMD finished (0 seconds)
-generating stats files
CMD: /usr/local/bin/util/..//Inchworm/bin/fastaToKmerCoverageStats --reads left.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 1 --DS > left.fa.K25.stats
CMD: /usr/local/bin/util/..//Inchworm/bin/fastaToKmerCoverageStats --reads right.fa --kmers jellyfish.K25.min2.kmers.fa --kmer_size 25 --num_threads 1 --DS > right.fa.K25.stats
-reading Kmer occurrences...
-reading Kmer occurrences...
done parsing 130857324 Kmers, 130857324 added, taking 175 seconds.
done parsing 130857324 Kmers, 130857324 added, taking 175 seconds.
STATS_GENERATION_TIME: 1611 seconds.
STATS_GENERATION_TIME: 1619 seconds.
CMD finished (1807 seconds)
CMD finished (1814 seconds)
CMD: touch left.fa.K25.stats.ok
CMD finished (0 seconds)
CMD: touch right.fa.K25.stats.ok
CMD finished (1 seconds)
-sorting each stats file by read name.
CMD: head -n1 left.fa.K25.stats > left.fa.K25.stats.sort && tail -n +2 left.fa.K25.stats | /usr/bin/sort --parallel=2 -k1,1 -T . -S 5G >> left.fa.K25.stats.sort
CMD: head -n1 right.fa.K25.stats > right.fa.K25.stats.sort && tail -n +2 right.fa.K25.stats | /usr/bin/sort --parallel=2 -k1,1 -T . -S 5G >> right.fa.K25.stats.sort
CMD finished (83 seconds)
CMD finished (96 seconds)
CMD: touch left.fa.K25.stats.sort.ok
CMD finished (0 seconds)
CMD: touch right.fa.K25.stats.sort.ok
CMD finished (1 seconds)
-defining normalized reads
CMD: /usr/local/bin/util/..//util/support_scripts//nbkc_merge_left_right_stats.pl --left left.fa.K25.stats.sort --right right.fa.K25.stats.sort --sorted > pairs.K25.stats
-opening left.fa.K25.stats.sort
-opening right.fa.K25.stats.sort
-done opening files.
CMD finished (711 seconds)
CMD: touch pairs.K25.stats.ok
CMD finished (0 seconds)
CMD: /usr/local/bin/util/..//util/support_scripts//nbkc_normalize.pl --stats_file pairs.K25.stats --max_cov 200 --min_cov 1 --max_CV 10000 > pairs.K25.stats.C200.maxCV10000.accs
22220886 / 37910906 = 58.61% reads selected during normalization.
0 / 37910906 = 0.00% reads discarded as likely aberrant based on coverage profiles.
0 / 37910906 = 0.00% reads discarded as below minimum coverage threshold=1
CMD finished (404 seconds)
CMD: touch pairs.K25.stats.C200.maxCV10000.accs.ok
CMD finished (0 seconds)
-search and capture.
-preparing to extract selected reads from: /home/ongchip/ongchip-DP/work/202408/A1_1_paired.fq.gz ... done prepping, now search and capture.
-capturing normalized reads from: /home/ongchip/ongchip-DP/work/202408/A1_1_paired.fq.gz
-preparing to extract selected reads from: /home/ongchip/ongchip-DP/work/202408/A1_2_paired.fq.gz ... done prepping, now search and capture.
-capturing normalized reads from: /home/ongchip/ongchip-DP/work/202408/A1_2_paired.fq.gz
CMD: touch /home/ongchip/ongchip-DP/work/202408/trinity_out_dir/insilico_read_normalization/A1_1_paired.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq.ok
CMD finished (0 seconds)
CMD: touch /home/ongchip/ongchip-DP/work/202408/trinity_out_dir/insilico_read_normalization/A1_2_paired.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq.ok
CMD finished (0 seconds)
CMD: ln -sf /home/ongchip/ongchip-DP/work/202408/trinity_out_dir/insilico_read_normalization/A1_1_paired.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq left.norm.fq
ln: failed to create symbolic link 'left.norm.fq': Operation not supported
Error, cmd: ln -sf /home/ongchip/ongchip-DP/work/202408/trinity_out_dir/insilico_read_normalization/A1_1_paired.fq.gz.normalized_K25_maxC200_minC1_maxCV10000.fq left.norm.fq died with ret 256 at /usr/local/bin/util/insilico_read_normalization.pl line 807.
Error, cmd: /usr/local/bin/util/insilico_read_normalization.pl --seqType fq --JM 10G --max_cov 200 --min_cov 1 --CPU 2 --output /home/ongchip/ongchip-DP/work/202408/trinity_out_dir/insilico_read_normalization --max_CV 10000 --left /home/ongchip/ongchip-DP/work/202408/A1_1_paired.fq.gz --right /home/ongchip/ongchip-DP/work/202408/A1_2_paired.fq.gz --pairs_together --PARALLEL_STATS died with ret 512 at /usr/local/bin/Trinity line 2919.
main::process_cmd("/usr/local/bin/util/insilico_read_normalization.pl --seqType "...) called at /usr/local/bin/Trinity line 3472
main::normalize("/home/ongchip/ongchip-DP/work/202408/trinity_out_dir/insilico"..., 200, ARRAY(0x56485ebfbe90), ARRAY(0x56485ebfbe78)) called at /usr/local/bin/Trinity line 3412
main::run_normalization(200, ARRAY(0x56485ebfbe90), ARRAY(0x56485ebfbe78)) called at /usr/local/bin/Trinity line 1450
Hello. De novo assembly analysis was performed with Trinity, but the analysis failed with the above message. I don't know what caused the error, and how to fix it. Please help me.
Thank you. Then should I commands like below?