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You were right, I had been working on that and fixed it alredy. Thanks.
Now, the featureCounts function says my files are .SAM, altought even checking on bash the class type its .BAM
It seems like it doesnt open the file and gives 0 count results.
RESULT:
I will keep looking for an answer on the web.
Thanks all for reading.
G.
Now, the featureCounts function says my files are .SAM, altought even checking on bash the class type its .BAM
It seems like it doesnt open the file and gives 0 count results.
RESULT:
Code:
//========================== featureCounts setting ===========================\\ || || || Input files : 8 SAM files || || S /home/sysadm/tomics/4_GCCAAT_L001_R1_001.f ... || || S /home/sysadm/tomics/8_AGTTCC_L001_R1_001.f ... || || S /home/sysadm/tomics/16_GCCAAT_L002_R1_001. ... || || S /home/sysadm/tomics/20_AGTTCC_L003_R1_001. ... || || S /home/sysadm/tomics/28_GCCAAT_L004_R1_001. ... || || S /home/sysadm/tomics/32_AGTTCC_L004_R1_001. ... || || S /home/sysadm/tomics/40_GCCAAT_L005_R1_001. ... || || S /home/sysadm/tomics/44_AGTTCC_L006_R1_001. ... || || || || Output file : ./.Rsubread_featureCounts_pid3679 || || Annotations : /home/sysadm/tomics/data3 (GTF) || || || || Threads : 1 || || Level : feature level || || Paired-end : no || || Strand specific : no || || Multimapping reads : not counted || || Multi-overlapping reads : not counted || || || \\===================== http://subread.sourceforge.net/ ======================// //================================= Running ==================================\\ || || || Load annotation file /home/sysadm/tomics/data3 ... || ^[[B^[[B|| Features : 1193694 || || Meta-features : 58174 || || Chromosomes : 25 || || || || Process SAM file /home/sysadm/tomics/4_GCCAAT_L001_R1_001.fastq.gz.sub ... || || Single-end reads are included. || || WARNING format issue in file '/home/sysadm/tomics/4_GCCAAT_L001_R1_001 ... || || The required format is : SAM || || The file format is unknown. || || A wrong format may result in wrong results or crash the program. || || Please refer to the manual for file format options. || || If the file is in the correct format, please ignore this message. || || || || Assign reads to features... || || Total reads : 2380011 || || Successfully assigned reads : 0 (0.0%) || || Running time : 0.02 minutes || || || || Process SAM file /home/sysadm/tomics/8_AGTTCC_L001_R1_001.fastq.gz.sub ... || || Single-end reads are included. || || WARNING format issue in file '/home/sysadm/tomics/8_AGTTCC_L001_R1_001 ... || || The required format is : SAM || || The file format is unknown. || || A wrong format may result in wrong results or crash the program. || || Please refer to the manual for file format options. || || If the file is in the correct format, please ignore this message. || || || || Assign reads to features... || || Total reads : 1956680 || || Successfully assigned reads : 0 (0.0%) || || Running time : 0.16 minutes || || || || Process SAM file /home/sysadm/tomics/16_GCCAAT_L002_R1_001.fastq.gz.su ... || || Single-end reads are included. || || WARNING format issue in file '/home/sysadm/tomics/16_GCCAAT_L002_R1_00 ... || || The required format is : SAM || || The file format is unknown. || || A wrong format may result in wrong results or crash the program. || || Please refer to the manual for file format options. || || If the file is in the correct format, please ignore this message. || || || || Assign reads to features... || || Total reads : 2287401 || || Successfully assigned reads : 0 (0.0%) || || Running time : 0.17 minutes || || || || Process SAM file /home/sysadm/tomics/20_AGTTCC_L003_R1_001.fastq.gz.su ... || || Single-end reads are included. || || WARNING format issue in file '/home/sysadm/tomics/20_AGTTCC_L003_R1_00 ... || || The required format is : SAM || || The file format is unknown. || || A wrong format may result in wrong results or crash the program. || || Please refer to the manual for file format options. || || If the file is in the correct format, please ignore this message. || || || || Assign reads to features... || || Total reads : 2362945 || || Successfully assigned reads : 0 (0.0%) || || Running time : 0.17 minutes || || || || Process SAM file /home/sysadm/tomics/28_GCCAAT_L004_R1_001.fastq.gz.su ... || || Single-end reads are included. || || WARNING format issue in file '/home/sysadm/tomics/28_GCCAAT_L004_R1_00 ... || || The required format is : SAM || || The file format is unknown. || || A wrong format may result in wrong results or crash the program. || || Please refer to the manual for file format options. || || If the file is in the correct format, please ignore this message. || || || || Assign reads to features... || || Total reads : 1884255 || || Successfully assigned reads : 0 (0.0%) || || Running time : 0.15 minutes || || || || Process SAM file /home/sysadm/tomics/32_AGTTCC_L004_R1_001.fastq.gz.su ... || || Single-end reads are included. || || WARNING format issue in file '/home/sysadm/tomics/32_AGTTCC_L004_R1_00 ... || || The required format is : SAM || || The file format is unknown. || || A wrong format may result in wrong results or crash the program. || || Please refer to the manual for file format options. || || If the file is in the correct format, please ignore this message. || || || || Assign reads to features... || || Total reads : 4205162 || || Successfully assigned reads : 0 (0.0%) || || Running time : 0.29 minutes || || || || Process SAM file /home/sysadm/tomics/40_GCCAAT_L005_R1_001.fastq.gz.su ... || || Single-end reads are included. || || WARNING format issue in file '/home/sysadm/tomics/40_GCCAAT_L005_R1_00 ... || || The required format is : SAM || || The file format is unknown. || || A wrong format may result in wrong results or crash the program. || || Please refer to the manual for file format options. || || If the file is in the correct format, please ignore this message. || || || || Assign reads to features... || || Total reads : 1953045 || || Successfully assigned reads : 0 (0.0%) || || Running time : 0.14 minutes || || || || Process SAM file /home/sysadm/tomics/44_AGTTCC_L006_R1_001.fastq.gz.su ... || || Single-end reads are included. || || WARNING format issue in file '/home/sysadm/tomics/44_AGTTCC_L006_R1_00 ... || || The required format is : SAM || || The file format is unknown. || || A wrong format may result in wrong results or crash the program. || || Please refer to the manual for file format options. || || If the file is in the correct format, please ignore this message. || || || || Assign reads to features... || || Total reads : 2908457 || || Successfully assigned reads : 0 (0.0%) || || Running time : 0.22 minutes || || || || Read assignment finished. || || || \\===================== http://subread.sourceforge.net/ ======================//
Thanks all for reading.
G.
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