Job ID = 10165670 SRX = SRX8331147 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 30081170 spots for SRR11778460/SRR11778460.sra Written 30081170 spots for SRR11778460/SRR11778460.sra fastq に変換しました。 bowtie でマッピング中... Your job 10165955 ("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: 00:10:14 30081170 reads; of these: 30081170 (100.00%) were unpaired; of these: 684867 (2.28%) aligned 0 times 24947261 (82.93%) aligned exactly 1 time 4449042 (14.79%) aligned >1 times 97.72% overall alignment rate Time searching: 00:10:14 Overall time: 00:10:14 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] 7603447 / 29396303 = 0.2587 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 19:53:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8331147/SRX8331147.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8331147/SRX8331147.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8331147/SRX8331147.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8331147/SRX8331147.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 19:53:34: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:53:34: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:53:40: 1000000 INFO @ Thu, 08 Oct 2020 19:53:46: 2000000 INFO @ Thu, 08 Oct 2020 19:53:52: 3000000 INFO @ Thu, 08 Oct 2020 19:53:58: 4000000 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 19:54:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8331147/SRX8331147.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8331147/SRX8331147.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8331147/SRX8331147.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8331147/SRX8331147.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 19:54:03: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:54:03: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:54:05: 5000000 INFO @ Thu, 08 Oct 2020 19:54:10: 1000000 INFO @ Thu, 08 Oct 2020 19:54:11: 6000000 INFO @ Thu, 08 Oct 2020 19:54:18: 2000000 INFO @ Thu, 08 Oct 2020 19:54:18: 7000000 INFO @ Thu, 08 Oct 2020 19:54:25: 8000000 INFO @ Thu, 08 Oct 2020 19:54:26: 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 19:54:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8331147/SRX8331147.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8331147/SRX8331147.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8331147/SRX8331147.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8331147/SRX8331147.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 19:54:31: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:54:31: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:54:32: 9000000 INFO @ Thu, 08 Oct 2020 19:54:33: 4000000 INFO @ Thu, 08 Oct 2020 19:54:39: 10000000 INFO @ Thu, 08 Oct 2020 19:54:39: 1000000 INFO @ Thu, 08 Oct 2020 19:54:41: 5000000 INFO @ Thu, 08 Oct 2020 19:54:46: 11000000 INFO @ Thu, 08 Oct 2020 19:54:47: 2000000 INFO @ Thu, 08 Oct 2020 19:54:48: 6000000 INFO @ Thu, 08 Oct 2020 19:54:53: 12000000 INFO @ Thu, 08 Oct 2020 19:54:54: 3000000 INFO @ Thu, 08 Oct 2020 19:54:56: 7000000 INFO @ Thu, 08 Oct 2020 19:55:00: 13000000 INFO @ Thu, 08 Oct 2020 19:55:02: 4000000 INFO @ Thu, 08 Oct 2020 19:55:03: 8000000 INFO @ Thu, 08 Oct 2020 19:55:07: 14000000 INFO @ Thu, 08 Oct 2020 19:55:09: 5000000 INFO @ Thu, 08 Oct 2020 19:55:11: 9000000 INFO @ Thu, 08 Oct 2020 19:55:14: 15000000 INFO @ Thu, 08 Oct 2020 19:55:17: 6000000 INFO @ Thu, 08 Oct 2020 19:55:18: 10000000 INFO @ Thu, 08 Oct 2020 19:55:21: 16000000 INFO @ Thu, 08 Oct 2020 19:55:24: 7000000 INFO @ Thu, 08 Oct 2020 19:55:26: 11000000 INFO @ Thu, 08 Oct 2020 19:55:28: 17000000 INFO @ Thu, 08 Oct 2020 19:55:32: 8000000 INFO @ Thu, 08 Oct 2020 19:55:34: 12000000 INFO @ Thu, 08 Oct 2020 19:55:35: 18000000 INFO @ Thu, 08 Oct 2020 19:55:39: 9000000 INFO @ Thu, 08 Oct 2020 19:55:41: 13000000 INFO @ Thu, 08 Oct 2020 19:55:43: 19000000 INFO @ Thu, 08 Oct 2020 19:55:47: 10000000 INFO @ Thu, 08 Oct 2020 19:55:49: 14000000 INFO @ Thu, 08 Oct 2020 19:55:50: 20000000 INFO @ Thu, 08 Oct 2020 19:55:55: 11000000 INFO @ Thu, 08 Oct 2020 19:55:57: 15000000 INFO @ Thu, 08 Oct 2020 19:55:57: 21000000 INFO @ Thu, 08 Oct 2020 19:56:02: #1 tag size is determined as 68 bps INFO @ Thu, 08 Oct 2020 19:56:02: #1 tag size = 68 INFO @ Thu, 08 Oct 2020 19:56:02: #1 total tags in treatment: 21792856 INFO @ Thu, 08 Oct 2020 19:56:02: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:56:02: #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 19:56:03: 12000000 INFO @ Thu, 08 Oct 2020 19:56:03: #1 tags after filtering in treatment: 21792856 INFO @ Thu, 08 Oct 2020 19:56:03: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:56:03: #1 finished! INFO @ Thu, 08 Oct 2020 19:56:03: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:56:03: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:56:04: #2 number of paired peaks: 149 WARNING @ Thu, 08 Oct 2020 19:56:04: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Thu, 08 Oct 2020 19:56:04: start model_add_line... INFO @ Thu, 08 Oct 2020 19:56:04: start X-correlation... INFO @ Thu, 08 Oct 2020 19:56:04: end of X-cor INFO @ Thu, 08 Oct 2020 19:56:04: #2 finished! INFO @ Thu, 08 Oct 2020 19:56:04: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 19:56:04: #2 alternative fragment length(s) may be 1,11,468,537 bps INFO @ Thu, 08 Oct 2020 19:56:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8331147/SRX8331147.05_model.r WARNING @ Thu, 08 Oct 2020 19:56:04: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 19:56:04: #2 You may need to consider one of the other alternative d(s): 1,11,468,537 WARNING @ Thu, 08 Oct 2020 19:56:04: #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 19:56:04: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:56:04: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:56:04: 16000000 INFO @ Thu, 08 Oct 2020 19:56:10: 13000000 INFO @ Thu, 08 Oct 2020 19:56:12: 17000000 INFO @ Thu, 08 Oct 2020 19:56:18: 14000000 INFO @ Thu, 08 Oct 2020 19:56:20: 18000000 INFO @ Thu, 08 Oct 2020 19:56:26: 15000000 INFO @ Thu, 08 Oct 2020 19:56:27: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 19:56:34: 16000000 INFO @ Thu, 08 Oct 2020 19:56:35: 20000000 INFO @ Thu, 08 Oct 2020 19:56:39: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:56:42: 17000000 INFO @ Thu, 08 Oct 2020 19:56:43: 21000000 INFO @ Thu, 08 Oct 2020 19:56:49: #1 tag size is determined as 68 bps INFO @ Thu, 08 Oct 2020 19:56:49: #1 tag size = 68 INFO @ Thu, 08 Oct 2020 19:56:49: #1 total tags in treatment: 21792856 INFO @ Thu, 08 Oct 2020 19:56:49: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:56:49: #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 19:56:49: #1 tags after filtering in treatment: 21792856 INFO @ Thu, 08 Oct 2020 19:56:49: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:56:49: #1 finished! INFO @ Thu, 08 Oct 2020 19:56:49: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:56:49: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:56:49: 18000000 INFO @ Thu, 08 Oct 2020 19:56:50: #2 number of paired peaks: 149 WARNING @ Thu, 08 Oct 2020 19:56:50: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Thu, 08 Oct 2020 19:56:50: start model_add_line... INFO @ Thu, 08 Oct 2020 19:56:50: start X-correlation... INFO @ Thu, 08 Oct 2020 19:56:50: end of X-cor INFO @ Thu, 08 Oct 2020 19:56:50: #2 finished! INFO @ Thu, 08 Oct 2020 19:56:50: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 19:56:50: #2 alternative fragment length(s) may be 1,11,468,537 bps INFO @ Thu, 08 Oct 2020 19:56:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8331147/SRX8331147.10_model.r WARNING @ Thu, 08 Oct 2020 19:56:50: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 19:56:50: #2 You may need to consider one of the other alternative d(s): 1,11,468,537 WARNING @ Thu, 08 Oct 2020 19:56:50: #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 19:56:50: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:56:50: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:56:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8331147/SRX8331147.05_peaks.xls INFO @ Thu, 08 Oct 2020 19:56:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8331147/SRX8331147.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:56:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8331147/SRX8331147.05_summits.bed INFO @ Thu, 08 Oct 2020 19:56:55: Done! INFO @ Thu, 08 Oct 2020 19:56:57: 19000000 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 19:57:04: 20000000 INFO @ Thu, 08 Oct 2020 19:57:11: 21000000 BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 19:57:17: #1 tag size is determined as 68 bps INFO @ Thu, 08 Oct 2020 19:57:17: #1 tag size = 68 INFO @ Thu, 08 Oct 2020 19:57:17: #1 total tags in treatment: 21792856 INFO @ Thu, 08 Oct 2020 19:57:17: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:57:17: #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 19:57:17: #1 tags after filtering in treatment: 21792856 INFO @ Thu, 08 Oct 2020 19:57:17: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:57:17: #1 finished! INFO @ Thu, 08 Oct 2020 19:57:17: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:57:17: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:57:19: #2 number of paired peaks: 149 WARNING @ Thu, 08 Oct 2020 19:57:19: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Thu, 08 Oct 2020 19:57:19: start model_add_line... INFO @ Thu, 08 Oct 2020 19:57:19: start X-correlation... INFO @ Thu, 08 Oct 2020 19:57:19: end of X-cor INFO @ Thu, 08 Oct 2020 19:57:19: #2 finished! INFO @ Thu, 08 Oct 2020 19:57:19: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 19:57:19: #2 alternative fragment length(s) may be 1,11,468,537 bps INFO @ Thu, 08 Oct 2020 19:57:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8331147/SRX8331147.20_model.r WARNING @ Thu, 08 Oct 2020 19:57:19: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 19:57:19: #2 You may need to consider one of the other alternative d(s): 1,11,468,537 WARNING @ Thu, 08 Oct 2020 19:57:19: #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 19:57:19: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:57:19: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:57:25: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:57:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8331147/SRX8331147.10_peaks.xls INFO @ Thu, 08 Oct 2020 19:57:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8331147/SRX8331147.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:57:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8331147/SRX8331147.10_summits.bed INFO @ Thu, 08 Oct 2020 19:57:41: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 19:57:54: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:58:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8331147/SRX8331147.20_peaks.xls INFO @ Thu, 08 Oct 2020 19:58:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8331147/SRX8331147.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:58:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8331147/SRX8331147.20_summits.bed INFO @ Thu, 08 Oct 2020 19:58:10: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling