Job ID = 10165665 SRX = SRX8331143 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 26926268 spots for SRR11778456/SRR11778456.sra Written 26926268 spots for SRR11778456/SRR11778456.sra fastq に変換しました。 bowtie でマッピング中... Your job 10165943 ("srTce11") 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: 00:09:15 26926268 reads; of these: 26926268 (100.00%) were unpaired; of these: 916201 (3.40%) aligned 0 times 22007076 (81.73%) aligned exactly 1 time 4002991 (14.87%) aligned >1 times 96.60% overall alignment rate Time searching: 00:09:15 Overall time: 00:09:15 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 11043440 / 26010067 = 0.4246 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 19:50:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8331143/SRX8331143.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8331143/SRX8331143.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8331143/SRX8331143.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8331143/SRX8331143.bam'] # control file = None # effective genome size = 9.00e+07 # 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 19:50:33: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:50:33: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:50:39: 1000000 INFO @ Thu, 08 Oct 2020 19:50:46: 2000000 INFO @ Thu, 08 Oct 2020 19:50:53: 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 19:51:00: 4000000 INFO @ Thu, 08 Oct 2020 19:51:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8331143/SRX8331143.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8331143/SRX8331143.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8331143/SRX8331143.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8331143/SRX8331143.bam'] # control file = None # effective genome size = 9.00e+07 # 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 19:51:03: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:51:03: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:51:08: 5000000 INFO @ Thu, 08 Oct 2020 19:51:10: 1000000 INFO @ Thu, 08 Oct 2020 19:51:15: 6000000 INFO @ Thu, 08 Oct 2020 19:51:17: 2000000 INFO @ Thu, 08 Oct 2020 19:51:23: 7000000 INFO @ Thu, 08 Oct 2020 19:51:24: 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 19:51:30: 8000000 INFO @ Thu, 08 Oct 2020 19:51:31: 4000000 INFO @ Thu, 08 Oct 2020 19:51:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8331143/SRX8331143.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8331143/SRX8331143.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8331143/SRX8331143.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8331143/SRX8331143.bam'] # control file = None # effective genome size = 9.00e+07 # 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 19:51:32: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:51:32: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:51:38: 9000000 INFO @ Thu, 08 Oct 2020 19:51:39: 5000000 INFO @ Thu, 08 Oct 2020 19:51:40: 1000000 INFO @ Thu, 08 Oct 2020 19:51:45: 10000000 INFO @ Thu, 08 Oct 2020 19:51:46: 6000000 INFO @ Thu, 08 Oct 2020 19:51:46: 2000000 INFO @ Thu, 08 Oct 2020 19:51:53: 11000000 INFO @ Thu, 08 Oct 2020 19:51:53: 3000000 INFO @ Thu, 08 Oct 2020 19:51:53: 7000000 INFO @ Thu, 08 Oct 2020 19:52:00: 12000000 INFO @ Thu, 08 Oct 2020 19:52:00: 4000000 INFO @ Thu, 08 Oct 2020 19:52:01: 8000000 INFO @ Thu, 08 Oct 2020 19:52:07: 5000000 INFO @ Thu, 08 Oct 2020 19:52:08: 13000000 INFO @ Thu, 08 Oct 2020 19:52:08: 9000000 INFO @ Thu, 08 Oct 2020 19:52:14: 6000000 INFO @ Thu, 08 Oct 2020 19:52:15: 10000000 INFO @ Thu, 08 Oct 2020 19:52:15: 14000000 INFO @ Thu, 08 Oct 2020 19:52:21: 7000000 INFO @ Thu, 08 Oct 2020 19:52:22: 11000000 INFO @ Thu, 08 Oct 2020 19:52:23: #1 tag size is determined as 74 bps INFO @ Thu, 08 Oct 2020 19:52:23: #1 tag size = 74 INFO @ Thu, 08 Oct 2020 19:52:23: #1 total tags in treatment: 14966627 INFO @ Thu, 08 Oct 2020 19:52:23: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:52:23: #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 19:52:23: #1 tags after filtering in treatment: 14966627 INFO @ Thu, 08 Oct 2020 19:52:23: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:52:23: #1 finished! INFO @ Thu, 08 Oct 2020 19:52:23: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:52:23: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:52:24: #2 number of paired peaks: 287 WARNING @ Thu, 08 Oct 2020 19:52:24: Fewer paired peaks (287) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 287 pairs to build model! INFO @ Thu, 08 Oct 2020 19:52:24: start model_add_line... INFO @ Thu, 08 Oct 2020 19:52:24: start X-correlation... INFO @ Thu, 08 Oct 2020 19:52:24: end of X-cor INFO @ Thu, 08 Oct 2020 19:52:24: #2 finished! INFO @ Thu, 08 Oct 2020 19:52:24: #2 predicted fragment length is 60 bps INFO @ Thu, 08 Oct 2020 19:52:24: #2 alternative fragment length(s) may be 2,60,573 bps INFO @ Thu, 08 Oct 2020 19:52:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8331143/SRX8331143.05_model.r WARNING @ Thu, 08 Oct 2020 19:52:24: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 19:52:24: #2 You may need to consider one of the other alternative d(s): 2,60,573 WARNING @ Thu, 08 Oct 2020 19:52:24: #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 19:52:24: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:52:24: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:52:28: 8000000 INFO @ Thu, 08 Oct 2020 19:52:30: 12000000 INFO @ Thu, 08 Oct 2020 19:52:34: 9000000 INFO @ Thu, 08 Oct 2020 19:52:38: 13000000 INFO @ Thu, 08 Oct 2020 19:52:41: 10000000 INFO @ Thu, 08 Oct 2020 19:52:46: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 19:52:47: 11000000 INFO @ Thu, 08 Oct 2020 19:52:51: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:52:53: #1 tag size is determined as 74 bps INFO @ Thu, 08 Oct 2020 19:52:53: #1 tag size = 74 INFO @ Thu, 08 Oct 2020 19:52:53: #1 total tags in treatment: 14966627 INFO @ Thu, 08 Oct 2020 19:52:53: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:52:53: #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 19:52:53: #1 tags after filtering in treatment: 14966627 INFO @ Thu, 08 Oct 2020 19:52:53: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:52:53: #1 finished! INFO @ Thu, 08 Oct 2020 19:52:53: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:52:53: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:52:54: 12000000 INFO @ Thu, 08 Oct 2020 19:52:54: #2 number of paired peaks: 287 WARNING @ Thu, 08 Oct 2020 19:52:54: Fewer paired peaks (287) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 287 pairs to build model! INFO @ Thu, 08 Oct 2020 19:52:54: start model_add_line... INFO @ Thu, 08 Oct 2020 19:52:54: start X-correlation... INFO @ Thu, 08 Oct 2020 19:52:54: end of X-cor INFO @ Thu, 08 Oct 2020 19:52:54: #2 finished! INFO @ Thu, 08 Oct 2020 19:52:54: #2 predicted fragment length is 60 bps INFO @ Thu, 08 Oct 2020 19:52:54: #2 alternative fragment length(s) may be 2,60,573 bps INFO @ Thu, 08 Oct 2020 19:52:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8331143/SRX8331143.10_model.r WARNING @ Thu, 08 Oct 2020 19:52:54: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 19:52:54: #2 You may need to consider one of the other alternative d(s): 2,60,573 WARNING @ Thu, 08 Oct 2020 19:52:54: #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 19:52:54: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:52:54: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:53:00: 13000000 INFO @ Thu, 08 Oct 2020 19:53:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8331143/SRX8331143.05_peaks.xls INFO @ Thu, 08 Oct 2020 19:53:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8331143/SRX8331143.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:53:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8331143/SRX8331143.05_summits.bed INFO @ Thu, 08 Oct 2020 19:53:04: Done! INFO @ Thu, 08 Oct 2020 19:53:06: 14000000 pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (662 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 19:53:12: #1 tag size is determined as 74 bps INFO @ Thu, 08 Oct 2020 19:53:12: #1 tag size = 74 INFO @ Thu, 08 Oct 2020 19:53:12: #1 total tags in treatment: 14966627 INFO @ Thu, 08 Oct 2020 19:53:12: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:53:12: #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 19:53:12: #1 tags after filtering in treatment: 14966627 INFO @ Thu, 08 Oct 2020 19:53:12: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:53:12: #1 finished! INFO @ Thu, 08 Oct 2020 19:53:12: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:53:12: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:53:13: #2 number of paired peaks: 287 WARNING @ Thu, 08 Oct 2020 19:53:13: Fewer paired peaks (287) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 287 pairs to build model! INFO @ Thu, 08 Oct 2020 19:53:13: start model_add_line... INFO @ Thu, 08 Oct 2020 19:53:13: start X-correlation... INFO @ Thu, 08 Oct 2020 19:53:13: end of X-cor INFO @ Thu, 08 Oct 2020 19:53:13: #2 finished! INFO @ Thu, 08 Oct 2020 19:53:13: #2 predicted fragment length is 60 bps INFO @ Thu, 08 Oct 2020 19:53:13: #2 alternative fragment length(s) may be 2,60,573 bps INFO @ Thu, 08 Oct 2020 19:53:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8331143/SRX8331143.20_model.r WARNING @ Thu, 08 Oct 2020 19:53:13: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 19:53:13: #2 You may need to consider one of the other alternative d(s): 2,60,573 WARNING @ Thu, 08 Oct 2020 19:53:13: #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 19:53:13: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:53:13: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:53:21: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 19:53:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8331143/SRX8331143.10_peaks.xls INFO @ Thu, 08 Oct 2020 19:53:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8331143/SRX8331143.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:53:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8331143/SRX8331143.10_summits.bed INFO @ Thu, 08 Oct 2020 19:53:33: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (460 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 19:53:42: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:53:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8331143/SRX8331143.20_peaks.xls INFO @ Thu, 08 Oct 2020 19:53:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8331143/SRX8331143.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:53:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8331143/SRX8331143.20_summits.bed INFO @ Thu, 08 Oct 2020 19:53:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (220 records, 4 fields): 1 millis CompletedMACS2peakCalling