TEMP ,Type checker found wrong number of fields while tokenizing data line.

Question

[rachid.fermi]

hello

I'm using this tool TEMP: a computational method for analyzing transposable element polymorphism in populations

I've tried the TEMP_absence.sh

bash ../scripts/TEMP_Absence.sh -i ./test_chromosome.sorted.bam -s ../scripts -r ./test_TE_annotation.bed -t ./dm3_chr2L.2bit

on test data and I got this error

Error: Type checker found wrong number of fields while tokenizing data line.
Perhaps you have extra TAB at the end of your line? Check with "cat -t"

I searched and found it might be caused by bedtools and I downgraded bedtools from 2.30 to 2.29 to 2.27 to 2.26 and still have the same error, but when i downgraded it to 2.25 I got a new error

Can't open test_chromosome.excision.cluster.rpmk.refined.bp.sfcp since No such file or directory

Since I'm using the tool on the test data provided by the tool it shouldn't raise any error

I'm using Ubuntu 16 and 20 I've tried in both laptops and got the same error

Can anyone please help me

[Ram]

What is the output to:

cat --show-all test_TE_annotation.bed

[rachid.fermi]

it shows this

> chr2L^I1301606^I1302488^IFBgn0001167_gypsy^I.^I-$
> chr2L^I2094501^I2094580^IFBgn0000155_roo^I.^I-$
> chr2L^I2100429^I2109522^IFBgn0000155_roo^I.^I-$
> chr2L^I2112167^I2118361^IFBgn0003007_opus^I.^I-$
> chr2L^I2118446^I2119772^IFBgn0003007_opus^I.^I-$
> chr2L^I2159453^I2159556^IFBgn0000155_roo^I.^I-$
> chr2L^I2267349^I2267457^IFBgn0000155_roo^I.^I+$
> chr2L^I2294096^I2299243^IFBgn0000349_copia^I.^I-$
> chr2L^I2378805^I2378893^IFBgn0000155_roo^I.^I+$
> chr2L^I2530303^I2530389^IFBgn0000155_roo^I.^I+$
> chr2L^I2565592^I2569028^IFBgn0000005_297^I.^I+$
> chr2L^I2565667^I2565886^IFBgn0000004_17.6^I.^I+$
> chr2L^I2565869^I2566006^IFBgn0063450_Tom1^I.^I+$
> chr2L^I2565871^I2566024^IFBgn0061485_rover^I.^I+$
> chr2L^I2565920^I2566024^IFBgn0063917_McClintock^I.^I+$
> chr2L^I2566158^I2569026^IFBgn0000004_17.6^I.^I+$
> chr2L^I2566674^I2566848^IFBgn0061485_rover^I.^I+$
> chr2L^I2567367^I2569022^IFBgn0061485_rover^I.^I+$
> chr2L^I2567598^I2567816^IFBgn0063917_McClintock^I.^I+$
> chr2L^I2567665^I2569027^IFBgn0044355_Quasimodo^I.^I+$
> chr2L^I2568060^I2569027^IFBgn0026065_Idefix^I.^I+$
> chr2L^I2568062^I2569018^IFBgn0063917_McClintock^I.^I+$
> chr2L^I2568070^I2569004^IFBgn0063447_accord^I.^I+$
> chr2L^I2568121^I2568988^IFBgn0004082_Tirant^I.^I+$
> chr2L^I2568137^I2569006^IFBgn0063432_gypsy5^I.^I+$
> chr2L^I2568137^I2568942^IFBgn0040267_Transpac^I.^I+$
> chr2L^I2568153^I2569001^IFBgn0063782_accord2^I.^I-$
> chr2L^I2568154^I2568990^IFBgn0023131_ZAM^I.^I+$
> chr2L^I2568193^I2568993^IFBgn0003007_opus^I.^I+$
> chr2L^I2568251^I2568697^IFBgn0000006_412^I.^I+$
> chr2L^I2568264^I2568985^IFBgn0063434_gypsy3^I.^I+$
> chr2L^I2568264^I2568985^IFBgn0003490_springer^I.^I+$
> chr2L^I2568308^I2568520^IFBgn0067387_gypsy10^I.^I+$
> chr2L^I2568308^I2568517^IFBgn0067384_gypsy7^I.^I+$
> chr2L^I2568308^I2568878^IFBgn0063431_gypsy6^I.^I+$
> chr2L^I2568308^I2568703^IFBgn0001167_gypsy^I.^I+$
> chr2L^I2568313^I2568828^IFBgn0002697_mdg1^I.^I+$
> chr2L^I2568313^I2568526^IFBgn0000199_blood^I.^I+$
> chr2L^I2568329^I2568982^IFBgnnnnnnnn_HMS-Beagle2^I.^I+$
> chr2L^I2568329^I2568982^IFBgn0001207_HMS-Beagle^I.^I+$
> chr2L^I2568378^I2568648^IFBgn0063897_Stalker4^I.^I+$
> chr2L^I2568378^I2568878^IFBgn0063433_gypsy4^I.^I+$
> chr2L^I2568384^I2568646^IFBgn0063435_gypsy2^I.^I+$
> chr2L^I2568384^I2568796^IFBgn0002698_mdg3^I.^I+$
> chr2L^I2569006^I2569756^IFBgn0063917_McClintock^I.^I+$
> chr2L^I2569007^I2571200^IFBgn0000004_17.6^I.^I+$
> chr2L^I2569010^I2571603^IFBgn0000005_297^I.^I+$
> chr2L^I2569018^I2569804^IFBgn0061485_rover^I.^I+$
> chr2L^I2569064^I2570806^IFBgn0044355_Quasimodo^I.^I+$
> chr2L^I2569064^I2569752^IFBgn0026065_Idefix^I.^I+$
> chr2L^I2569859^I2571024^IFBgn0061485_rover^I.^I+$
> chr2L^I2569987^I2570809^IFBgn0026065_Idefix^I.^I+$
> chr2L^I2570511^I2570703^IFBgn0063917_McClintock^I.^I+$
> chr2L^I2571048^I2571200^IFBgn0063917_McClintock^I.^I+$
> chr2L^I2571264^I2571483^IFBgn0000004_17.6^I.^I+$
> chr2L^I2571466^I2571603^IFBgn0063450_Tom1^I.^I+$
> chr2L^I2571468^I2571592^IFBgn0061485_rover^I.^I+$
> chr2L^I2661257^I2663012^IFBgn0001249_I-element^I.^I+$
> chr2L^I2713413^I2713444^IFBgn0063371_transib2^I.^I-$
> chr2L^I2772652^I2776969^IFBgn0000005_297^I.^I+$
> chr2L^I2772727^I2772946^IFBgn0000004_17.6^I.^I+$
> chr2L^I2772929^I2773066^IFBgn0063450_Tom1^I.^I+$
> chr2L^I2772931^I2773084^IFBgn0061485_rover^I.^I+$
> chr2L^I2772980^I2773084^IFBgn0063917_McClintock^I.^I+$
> chr2L^I2773736^I2773910^IFBgn0061485_rover^I.^I+$
> chr2L^I2774429^I2776968^IFBgn0061485_rover^I.^I+$
> chr2L^I2774429^I2776968^IFBgn0000004_17.6^I.^I+$
> chr2L^I2774660^I2774878^IFBgn0063917_McClintock^I.^I+$
> chr2L^I2774727^I2776980^IFBgn0044355_Quasimodo^I.^I+$
> chr2L^I2775122^I2776985^IFBgn0026065_Idefix^I.^I+$
> chr2L^I2775124^I2776969^IFBgn0063917_McClintock^I.^I+$
> chr2L^I2775132^I2776531^IFBgn0063447_accord^I.^I+$
> chr2L^I2775183^I2776509^IFBgn0004082_Tirant^I.^I+$
> chr2L^I2775199^I2776553^IFBgn0063432_gypsy5^I.^I+$
> chr2L^I2775199^I2776494^IFBgn0040267_Transpac^I.^I+$
> chr2L^I2775215^I2776321^IFBgn0063782_accord2^I.^I-$
> chr2L^I2775216^I2776513^IFBgn0023131_ZAM^I.^I+$
> chr2L^I2775255^I2776055^IFBgn0003007_opus^I.^I+$
> chr2L^I2775313^I2775759^IFBgn0000006_412^I.^I+$
> chr2L^I2775326^I2776047^IFBgn0063434_gypsy3^I.^I+$
> chr2L^I2775326^I2776047^IFBgn0003490_springer^I.^I+$
> chr2L^I2775370^I2775579^IFBgn0067384_gypsy7^I.^I+$
> chr2L^I2775370^I2775765^IFBgn0001167_gypsy^I.^I+$
> chr2L^I2775375^I2775890^IFBgn0002697_mdg1^I.^I+$
> chr2L^I2775375^I2775588^IFBgn0000199_blood^I.^I+$
> chr2L^I2775391^I2776044^IFBgnnnnnnnn_HMS-Beagle2^I.^I+$
> chr2L^I2775391^I2776044^IFBgn0001207_HMS-Beagle^I.^I+$
> chr2L^I2775429^I2775767^IFBgn0010302_Burdock^I.^I+$
> chr2L^I2775440^I2775710^IFBgn0063897_Stalker4^I.^I+$
> chr2L^I2775440^I2776515^IFBgn0063433_gypsy4^I.^I+$
> chr2L^I2775442^I2775582^IFBgn0067387_gypsy10^I.^I+$
> chr2L^I2775446^I2775858^IFBgn0002698_mdg3^I.^I+$
> chr2L^I2776093^I2776340^IFBgn0000199_blood^I.^I+$
> chr2L^I2776099^I2776519^IFBgnnnnnnnn_HMS-Beagle2^I.^I+$
> chr2L^I2776156^I2776324^IFBgn0063436_gtwin^I.^I+$
> chr2L^I2776156^I2776516^IFBgn0063431_gypsy6^I.^I+$
> chr2L^I2776179^I2776389^IFBgn0003007_opus^I.^I+$
> chr2L^I2776938^I2777318^IFBgn0063917_McClintock^I.^I+$
> chr2L^I2776958^I2777320^IFBgn0000004_17.6^I.^I+$
> chr2L^I2776962^I2777324^IFBgn0061485_rover^I.^I+$
> chr2L^I2776962^I2777324^IFBgn0000005_297^I.^I+$
> chr2L^I2776975^I2777315^IFBgn0044355_Quasimodo^I.^I+$
> chr2L^I2777321^I2779175^IFBgn0000005_297^I.^I+$
> chr2L^I2777323^I2778772^IFBgn0000004_17.6^I.^I+$
> chr2L^I2777510^I2778596^IFBgn0061485_rover^I.^I+$
> chr2L^I2777559^I2778381^IFBgn0026065_Idefix^I.^I+$
> chr2L^I2777565^I2778378^IFBgn0044355_Quasimodo^I.^I+$
> chr2L^I2778083^I2778275^IFBgn0063917_McClintock^I.^I+$
> chr2L^I2778620^I2778772^IFBgn0063917_McClintock^I.^I+$
> chr2L^I2778836^I2779055^IFBgn0000004_17.6^I.^I+$
> chr2L^I2779038^I2779175^IFBgn0063450_Tom1^I.^I+$
> chr2L^I2779040^I2779164^IFBgn0061485_rover^I.^I+$
> chr2L^I2933353^I2935475^IFBgn0003122_pogo^I.^I-$
> chr2L^I2945631^I2945785^IFBgn0000155_roo^I.^I+$
> chr2L^I2963474^I2963538^IFBgn0000155_roo^I.^I+$

Answer 1

[rachid.fermi]

i fixed this issue i had to downgrade samtools and bedtools

• samtools version 1.4
• bedtools bersion 2.25