Job ID = 10166221 SRX = SRX7723716 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 20054790 spots for SRR11084672/SRR11084672.sra Written 20054790 spots for SRR11084672/SRR11084672.sra fastq に変換しました。 bowtie でマッピング中... Your job 10166576 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:57 20054790 reads; of these: 20054790 (100.00%) were unpaired; of these: 12505085 (62.35%) aligned 0 times 5622446 (28.04%) aligned exactly 1 time 1927259 (9.61%) aligned >1 times 37.65% overall alignment rate Time searching: 00:04:57 Overall time: 00:04:57 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 2508457 / 7549705 = 0.3323 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:49:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723716/SRX7723716.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723716/SRX7723716.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723716/SRX7723716.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723716/SRX7723716.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Thu, 08 Oct 2020 20:49:12: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:49:12: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:49:19: 1000000 INFO @ Thu, 08 Oct 2020 20:49:26: 2000000 INFO @ Thu, 08 Oct 2020 20:49:33: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:49:40: 4000000 INFO @ Thu, 08 Oct 2020 20:49:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723716/SRX7723716.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723716/SRX7723716.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723716/SRX7723716.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723716/SRX7723716.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Thu, 08 Oct 2020 20:49:46: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:49:46: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:49:47: 5000000 INFO @ Thu, 08 Oct 2020 20:49:47: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 20:49:47: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 20:49:47: #1 total tags in treatment: 5041248 INFO @ Thu, 08 Oct 2020 20:49:47: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:49:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:49:47: #1 tags after filtering in treatment: 5041248 INFO @ Thu, 08 Oct 2020 20:49:47: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:49:47: #1 finished! INFO @ Thu, 08 Oct 2020 20:49:47: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:49:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:49:47: #2 number of paired peaks: 114 WARNING @ Thu, 08 Oct 2020 20:49:47: Fewer paired peaks (114) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 114 pairs to build model! INFO @ Thu, 08 Oct 2020 20:49:47: start model_add_line... INFO @ Thu, 08 Oct 2020 20:49:47: start X-correlation... INFO @ Thu, 08 Oct 2020 20:49:47: end of X-cor INFO @ Thu, 08 Oct 2020 20:49:47: #2 finished! INFO @ Thu, 08 Oct 2020 20:49:47: #2 predicted fragment length is 120 bps INFO @ Thu, 08 Oct 2020 20:49:47: #2 alternative fragment length(s) may be 120 bps INFO @ Thu, 08 Oct 2020 20:49:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723716/SRX7723716.05_model.r WARNING @ Thu, 08 Oct 2020 20:49:47: #2 Since the d (120) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:49:47: #2 You may need to consider one of the other alternative d(s): 120 WARNING @ Thu, 08 Oct 2020 20:49:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:49:47: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:49:47: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:49:52: 1000000 INFO @ Thu, 08 Oct 2020 20:49:58: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:49:59: 2000000 INFO @ Thu, 08 Oct 2020 20:50:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723716/SRX7723716.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:50:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723716/SRX7723716.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:50:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723716/SRX7723716.05_summits.bed INFO @ Thu, 08 Oct 2020 20:50:04: Done! INFO @ Thu, 08 Oct 2020 20:50:05: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:50:11: 4000000 INFO @ Thu, 08 Oct 2020 20:50:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723716/SRX7723716.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723716/SRX7723716.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723716/SRX7723716.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723716/SRX7723716.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Thu, 08 Oct 2020 20:50:15: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:50:15: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:50:17: 5000000 INFO @ Thu, 08 Oct 2020 20:50:17: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 20:50:17: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 20:50:17: #1 total tags in treatment: 5041248 INFO @ Thu, 08 Oct 2020 20:50:17: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:50:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:50:17: #1 tags after filtering in treatment: 5041248 INFO @ Thu, 08 Oct 2020 20:50:17: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:50:17: #1 finished! INFO @ Thu, 08 Oct 2020 20:50:17: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:50:17: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:50:18: #2 number of paired peaks: 114 WARNING @ Thu, 08 Oct 2020 20:50:18: Fewer paired peaks (114) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 114 pairs to build model! INFO @ Thu, 08 Oct 2020 20:50:18: start model_add_line... INFO @ Thu, 08 Oct 2020 20:50:18: start X-correlation... INFO @ Thu, 08 Oct 2020 20:50:18: end of X-cor INFO @ Thu, 08 Oct 2020 20:50:18: #2 finished! INFO @ Thu, 08 Oct 2020 20:50:18: #2 predicted fragment length is 120 bps INFO @ Thu, 08 Oct 2020 20:50:18: #2 alternative fragment length(s) may be 120 bps INFO @ Thu, 08 Oct 2020 20:50:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723716/SRX7723716.10_model.r WARNING @ Thu, 08 Oct 2020 20:50:18: #2 Since the d (120) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:50:18: #2 You may need to consider one of the other alternative d(s): 120 WARNING @ Thu, 08 Oct 2020 20:50:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:50:18: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:50:18: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (658 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:50:22: 1000000 INFO @ Thu, 08 Oct 2020 20:50:29: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:50:30: 2000000 INFO @ Thu, 08 Oct 2020 20:50:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723716/SRX7723716.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:50:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723716/SRX7723716.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:50:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723716/SRX7723716.10_summits.bed INFO @ Thu, 08 Oct 2020 20:50:34: Done! BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:50:37: 3000000 INFO @ Thu, 08 Oct 2020 20:50:44: 4000000 BigWig に変換しました。 pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (355 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:50:51: 5000000 INFO @ Thu, 08 Oct 2020 20:50:52: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 20:50:52: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 20:50:52: #1 total tags in treatment: 5041248 INFO @ Thu, 08 Oct 2020 20:50:52: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:50:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:50:52: #1 tags after filtering in treatment: 5041248 INFO @ Thu, 08 Oct 2020 20:50:52: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:50:52: #1 finished! INFO @ Thu, 08 Oct 2020 20:50:52: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:50:52: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:50:52: #2 number of paired peaks: 114 WARNING @ Thu, 08 Oct 2020 20:50:52: Fewer paired peaks (114) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 114 pairs to build model! INFO @ Thu, 08 Oct 2020 20:50:52: start model_add_line... INFO @ Thu, 08 Oct 2020 20:50:52: start X-correlation... INFO @ Thu, 08 Oct 2020 20:50:52: end of X-cor INFO @ Thu, 08 Oct 2020 20:50:52: #2 finished! INFO @ Thu, 08 Oct 2020 20:50:52: #2 predicted fragment length is 120 bps INFO @ Thu, 08 Oct 2020 20:50:52: #2 alternative fragment length(s) may be 120 bps INFO @ Thu, 08 Oct 2020 20:50:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723716/SRX7723716.20_model.r WARNING @ Thu, 08 Oct 2020 20:50:52: #2 Since the d (120) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:50:52: #2 You may need to consider one of the other alternative d(s): 120 WARNING @ Thu, 08 Oct 2020 20:50:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:50:52: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:50:52: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:51:03: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:51:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723716/SRX7723716.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:51:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723716/SRX7723716.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:51:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723716/SRX7723716.20_summits.bed INFO @ Thu, 08 Oct 2020 20:51:09: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (176 records, 4 fields): 3 millis CompletedMACS2peakCalling