Job ID = 10166085 SRX = SRX9120611 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:30 39221397 reads; of these: 39221397 (100.00%) were unpaired; of these: 12066185 (30.76%) aligned 0 times 22322391 (56.91%) aligned exactly 1 time 4832821 (12.32%) aligned >1 times 69.24% overall alignment rate Time searching: 00:07:30 Overall time: 00:07:30 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] 4979471 / 27155212 = 0.1834 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 20:42:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9120611/SRX9120611.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9120611/SRX9120611.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9120611/SRX9120611.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9120611/SRX9120611.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 20:42:04: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:42:04: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:42:09: 1000000 INFO @ Thu, 08 Oct 2020 20:42:15: 2000000 INFO @ Thu, 08 Oct 2020 20:42:20: 3000000 INFO @ Thu, 08 Oct 2020 20:42:26: 4000000 INFO @ Thu, 08 Oct 2020 20:42:31: 5000000 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 20:42:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9120611/SRX9120611.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9120611/SRX9120611.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9120611/SRX9120611.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9120611/SRX9120611.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 20:42:34: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:42:34: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:42:37: 6000000 INFO @ Thu, 08 Oct 2020 20:42:41: 1000000 INFO @ Thu, 08 Oct 2020 20:42:44: 7000000 INFO @ Thu, 08 Oct 2020 20:42:48: 2000000 INFO @ Thu, 08 Oct 2020 20:42:50: 8000000 INFO @ Thu, 08 Oct 2020 20:42:56: 3000000 INFO @ Thu, 08 Oct 2020 20:42:57: 9000000 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 20:43:03: 10000000 INFO @ Thu, 08 Oct 2020 20:43:03: 4000000 INFO @ Thu, 08 Oct 2020 20:43:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9120611/SRX9120611.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9120611/SRX9120611.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9120611/SRX9120611.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9120611/SRX9120611.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 20:43:04: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:43:04: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:43:10: 11000000 INFO @ Thu, 08 Oct 2020 20:43:11: 1000000 INFO @ Thu, 08 Oct 2020 20:43:11: 5000000 INFO @ Thu, 08 Oct 2020 20:43:16: 12000000 INFO @ Thu, 08 Oct 2020 20:43:17: 2000000 INFO @ Thu, 08 Oct 2020 20:43:18: 6000000 INFO @ Thu, 08 Oct 2020 20:43:22: 13000000 INFO @ Thu, 08 Oct 2020 20:43:24: 3000000 INFO @ Thu, 08 Oct 2020 20:43:25: 7000000 INFO @ Thu, 08 Oct 2020 20:43:29: 14000000 INFO @ Thu, 08 Oct 2020 20:43:31: 4000000 INFO @ Thu, 08 Oct 2020 20:43:33: 8000000 INFO @ Thu, 08 Oct 2020 20:43:35: 15000000 INFO @ Thu, 08 Oct 2020 20:43:38: 5000000 INFO @ Thu, 08 Oct 2020 20:43:40: 9000000 INFO @ Thu, 08 Oct 2020 20:43:42: 16000000 INFO @ Thu, 08 Oct 2020 20:43:44: 6000000 INFO @ Thu, 08 Oct 2020 20:43:47: 10000000 INFO @ Thu, 08 Oct 2020 20:43:48: 17000000 INFO @ Thu, 08 Oct 2020 20:43:51: 7000000 INFO @ Thu, 08 Oct 2020 20:43:54: 11000000 INFO @ Thu, 08 Oct 2020 20:43:55: 18000000 INFO @ Thu, 08 Oct 2020 20:43:58: 8000000 INFO @ Thu, 08 Oct 2020 20:44:01: 12000000 INFO @ Thu, 08 Oct 2020 20:44:02: 19000000 INFO @ Thu, 08 Oct 2020 20:44:05: 9000000 INFO @ Thu, 08 Oct 2020 20:44:08: 13000000 INFO @ Thu, 08 Oct 2020 20:44:09: 20000000 INFO @ Thu, 08 Oct 2020 20:44:11: 10000000 INFO @ Thu, 08 Oct 2020 20:44:15: 14000000 INFO @ Thu, 08 Oct 2020 20:44:15: 21000000 INFO @ Thu, 08 Oct 2020 20:44:18: 11000000 INFO @ Thu, 08 Oct 2020 20:44:22: 15000000 INFO @ Thu, 08 Oct 2020 20:44:22: 22000000 INFO @ Thu, 08 Oct 2020 20:44:23: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:44:23: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:44:23: #1 total tags in treatment: 22175741 INFO @ Thu, 08 Oct 2020 20:44:23: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:44:23: #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 20:44:24: #1 tags after filtering in treatment: 22175741 INFO @ Thu, 08 Oct 2020 20:44:24: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:44:24: #1 finished! INFO @ Thu, 08 Oct 2020 20:44:24: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:44:24: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:44:25: 12000000 INFO @ Thu, 08 Oct 2020 20:44:25: #2 number of paired peaks: 200 WARNING @ Thu, 08 Oct 2020 20:44:25: Fewer paired peaks (200) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 200 pairs to build model! INFO @ Thu, 08 Oct 2020 20:44:25: start model_add_line... INFO @ Thu, 08 Oct 2020 20:44:25: start X-correlation... INFO @ Thu, 08 Oct 2020 20:44:25: end of X-cor INFO @ Thu, 08 Oct 2020 20:44:25: #2 finished! INFO @ Thu, 08 Oct 2020 20:44:25: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:44:25: #2 alternative fragment length(s) may be 1,45 bps INFO @ Thu, 08 Oct 2020 20:44:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120611/SRX9120611.05_model.r WARNING @ Thu, 08 Oct 2020 20:44:25: #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 20:44:25: #2 You may need to consider one of the other alternative d(s): 1,45 WARNING @ Thu, 08 Oct 2020 20:44:25: #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 20:44:25: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:44:25: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:44:29: 16000000 INFO @ Thu, 08 Oct 2020 20:44:31: 13000000 INFO @ Thu, 08 Oct 2020 20:44:35: 17000000 INFO @ Thu, 08 Oct 2020 20:44:38: 14000000 INFO @ Thu, 08 Oct 2020 20:44:42: 18000000 INFO @ Thu, 08 Oct 2020 20:44:44: 15000000 INFO @ Thu, 08 Oct 2020 20:44:49: 19000000 INFO @ Thu, 08 Oct 2020 20:44:50: 16000000 INFO @ Thu, 08 Oct 2020 20:44:56: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:44:57: 17000000 INFO @ Thu, 08 Oct 2020 20:45:01: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:45:02: 21000000 INFO @ Thu, 08 Oct 2020 20:45:03: 18000000 INFO @ Thu, 08 Oct 2020 20:45:09: 22000000 INFO @ Thu, 08 Oct 2020 20:45:09: 19000000 INFO @ Thu, 08 Oct 2020 20:45:10: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:45:10: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:45:10: #1 total tags in treatment: 22175741 INFO @ Thu, 08 Oct 2020 20:45:10: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:45:10: #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 20:45:11: #1 tags after filtering in treatment: 22175741 INFO @ Thu, 08 Oct 2020 20:45:11: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:45:11: #1 finished! INFO @ Thu, 08 Oct 2020 20:45:11: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:45:11: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:45:12: #2 number of paired peaks: 200 WARNING @ Thu, 08 Oct 2020 20:45:12: Fewer paired peaks (200) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 200 pairs to build model! INFO @ Thu, 08 Oct 2020 20:45:12: start model_add_line... INFO @ Thu, 08 Oct 2020 20:45:12: start X-correlation... INFO @ Thu, 08 Oct 2020 20:45:12: end of X-cor INFO @ Thu, 08 Oct 2020 20:45:12: #2 finished! INFO @ Thu, 08 Oct 2020 20:45:12: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:45:12: #2 alternative fragment length(s) may be 1,45 bps INFO @ Thu, 08 Oct 2020 20:45:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120611/SRX9120611.10_model.r WARNING @ Thu, 08 Oct 2020 20:45:12: #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 20:45:12: #2 You may need to consider one of the other alternative d(s): 1,45 WARNING @ Thu, 08 Oct 2020 20:45:12: #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 20:45:12: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:45:12: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:45:16: 20000000 INFO @ Thu, 08 Oct 2020 20:45:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120611/SRX9120611.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:45:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120611/SRX9120611.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:45:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120611/SRX9120611.05_summits.bed INFO @ Thu, 08 Oct 2020 20:45:17: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:45:21: 21000000 INFO @ Thu, 08 Oct 2020 20:45:27: 22000000 INFO @ Thu, 08 Oct 2020 20:45:28: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:45:28: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:45:28: #1 total tags in treatment: 22175741 INFO @ Thu, 08 Oct 2020 20:45:28: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:45:28: #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 20:45:28: #1 tags after filtering in treatment: 22175741 INFO @ Thu, 08 Oct 2020 20:45:28: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:45:28: #1 finished! INFO @ Thu, 08 Oct 2020 20:45:28: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:45:28: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:45:29: #2 number of paired peaks: 200 WARNING @ Thu, 08 Oct 2020 20:45:29: Fewer paired peaks (200) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 200 pairs to build model! INFO @ Thu, 08 Oct 2020 20:45:29: start model_add_line... INFO @ Thu, 08 Oct 2020 20:45:30: start X-correlation... INFO @ Thu, 08 Oct 2020 20:45:30: end of X-cor INFO @ Thu, 08 Oct 2020 20:45:30: #2 finished! INFO @ Thu, 08 Oct 2020 20:45:30: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:45:30: #2 alternative fragment length(s) may be 1,45 bps INFO @ Thu, 08 Oct 2020 20:45:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120611/SRX9120611.20_model.r WARNING @ Thu, 08 Oct 2020 20:45:30: #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 20:45:30: #2 You may need to consider one of the other alternative d(s): 1,45 WARNING @ Thu, 08 Oct 2020 20:45:30: #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 20:45:30: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:45:30: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:45:46: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:46:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120611/SRX9120611.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:46:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120611/SRX9120611.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:46:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120611/SRX9120611.10_summits.bed INFO @ Thu, 08 Oct 2020 20:46:02: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:46:03: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:46:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120611/SRX9120611.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:46:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120611/SRX9120611.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:46:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120611/SRX9120611.20_summits.bed INFO @ Thu, 08 Oct 2020 20:46:20: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling