Job ID = 10165916 SRX = SRX6799193 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: 00:10:22 37378121 reads; of these: 37378121 (100.00%) were unpaired; of these: 1961769 (5.25%) aligned 0 times 25266821 (67.60%) aligned exactly 1 time 10149531 (27.15%) aligned >1 times 94.75% overall alignment rate Time searching: 00:10:22 Overall time: 00:10:22 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 16 files... [bam_rmdupse_core] 11216613 / 35416352 = 0.3167 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 20:27:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6799193/SRX6799193.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6799193/SRX6799193.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6799193/SRX6799193.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6799193/SRX6799193.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 20:27:06: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:27:06: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:27:13: 1000000 INFO @ Thu, 08 Oct 2020 20:27:19: 2000000 INFO @ Thu, 08 Oct 2020 20:27:26: 3000000 INFO @ Thu, 08 Oct 2020 20:27:33: 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 20:27:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6799193/SRX6799193.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6799193/SRX6799193.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6799193/SRX6799193.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6799193/SRX6799193.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 20:27:36: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:27:36: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:27:40: 5000000 INFO @ Thu, 08 Oct 2020 20:27:43: 1000000 INFO @ Thu, 08 Oct 2020 20:27:46: 6000000 INFO @ Thu, 08 Oct 2020 20:27:49: 2000000 INFO @ Thu, 08 Oct 2020 20:27:53: 7000000 INFO @ Thu, 08 Oct 2020 20:27:56: 3000000 INFO @ Thu, 08 Oct 2020 20:28:00: 8000000 INFO @ Thu, 08 Oct 2020 20:28:03: 4000000 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 20:28:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6799193/SRX6799193.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6799193/SRX6799193.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6799193/SRX6799193.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6799193/SRX6799193.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 20:28:06: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:28:06: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:28:07: 9000000 INFO @ Thu, 08 Oct 2020 20:28:09: 5000000 INFO @ Thu, 08 Oct 2020 20:28:13: 1000000 INFO @ Thu, 08 Oct 2020 20:28:13: 10000000 INFO @ Thu, 08 Oct 2020 20:28:16: 6000000 INFO @ Thu, 08 Oct 2020 20:28:19: 2000000 INFO @ Thu, 08 Oct 2020 20:28:20: 11000000 INFO @ Thu, 08 Oct 2020 20:28:23: 7000000 INFO @ Thu, 08 Oct 2020 20:28:26: 3000000 INFO @ Thu, 08 Oct 2020 20:28:27: 12000000 INFO @ Thu, 08 Oct 2020 20:28:30: 8000000 INFO @ Thu, 08 Oct 2020 20:28:33: 4000000 INFO @ Thu, 08 Oct 2020 20:28:33: 13000000 INFO @ Thu, 08 Oct 2020 20:28:36: 9000000 INFO @ Thu, 08 Oct 2020 20:28:40: 14000000 INFO @ Thu, 08 Oct 2020 20:28:40: 5000000 INFO @ Thu, 08 Oct 2020 20:28:43: 10000000 INFO @ Thu, 08 Oct 2020 20:28:46: 15000000 INFO @ Thu, 08 Oct 2020 20:28:47: 6000000 INFO @ Thu, 08 Oct 2020 20:28:50: 11000000 INFO @ Thu, 08 Oct 2020 20:28:53: 16000000 INFO @ Thu, 08 Oct 2020 20:28:53: 7000000 INFO @ Thu, 08 Oct 2020 20:28:56: 12000000 INFO @ Thu, 08 Oct 2020 20:29:00: 17000000 INFO @ Thu, 08 Oct 2020 20:29:00: 8000000 INFO @ Thu, 08 Oct 2020 20:29:02: 13000000 INFO @ Thu, 08 Oct 2020 20:29:06: 18000000 INFO @ Thu, 08 Oct 2020 20:29:07: 9000000 INFO @ Thu, 08 Oct 2020 20:29:09: 14000000 INFO @ Thu, 08 Oct 2020 20:29:13: 19000000 INFO @ Thu, 08 Oct 2020 20:29:14: 10000000 INFO @ Thu, 08 Oct 2020 20:29:15: 15000000 INFO @ Thu, 08 Oct 2020 20:29:20: 20000000 INFO @ Thu, 08 Oct 2020 20:29:20: 11000000 INFO @ Thu, 08 Oct 2020 20:29:22: 16000000 INFO @ Thu, 08 Oct 2020 20:29:26: 21000000 INFO @ Thu, 08 Oct 2020 20:29:27: 12000000 INFO @ Thu, 08 Oct 2020 20:29:29: 17000000 INFO @ Thu, 08 Oct 2020 20:29:33: 22000000 INFO @ Thu, 08 Oct 2020 20:29:33: 13000000 INFO @ Thu, 08 Oct 2020 20:29:35: 18000000 INFO @ Thu, 08 Oct 2020 20:29:39: 23000000 INFO @ Thu, 08 Oct 2020 20:29:40: 14000000 INFO @ Thu, 08 Oct 2020 20:29:42: 19000000 INFO @ Thu, 08 Oct 2020 20:29:46: 24000000 INFO @ Thu, 08 Oct 2020 20:29:46: 15000000 INFO @ Thu, 08 Oct 2020 20:29:47: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:29:47: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:29:47: #1 total tags in treatment: 24199739 INFO @ Thu, 08 Oct 2020 20:29:47: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:29:47: #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 20:29:48: #1 tags after filtering in treatment: 24199739 INFO @ Thu, 08 Oct 2020 20:29:48: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:29:48: #1 finished! INFO @ Thu, 08 Oct 2020 20:29:48: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:29:48: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:29:48: 20000000 INFO @ Thu, 08 Oct 2020 20:29:49: #2 number of paired peaks: 322 WARNING @ Thu, 08 Oct 2020 20:29:49: Fewer paired peaks (322) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 322 pairs to build model! INFO @ Thu, 08 Oct 2020 20:29:49: start model_add_line... INFO @ Thu, 08 Oct 2020 20:29:50: start X-correlation... INFO @ Thu, 08 Oct 2020 20:29:50: end of X-cor INFO @ Thu, 08 Oct 2020 20:29:50: #2 finished! INFO @ Thu, 08 Oct 2020 20:29:50: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:29:50: #2 alternative fragment length(s) may be 1,11,598 bps INFO @ Thu, 08 Oct 2020 20:29:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6799193/SRX6799193.05_model.r WARNING @ Thu, 08 Oct 2020 20:29:50: #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 20:29:50: #2 You may need to consider one of the other alternative d(s): 1,11,598 WARNING @ Thu, 08 Oct 2020 20:29:50: #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 20:29:50: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:29:50: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:29:53: 16000000 INFO @ Thu, 08 Oct 2020 20:29:55: 21000000 INFO @ Thu, 08 Oct 2020 20:29:59: 17000000 INFO @ Thu, 08 Oct 2020 20:30:01: 22000000 INFO @ Thu, 08 Oct 2020 20:30:06: 18000000 INFO @ Thu, 08 Oct 2020 20:30:08: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:30:13: 19000000 INFO @ Thu, 08 Oct 2020 20:30:14: 24000000 INFO @ Thu, 08 Oct 2020 20:30:16: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:30:16: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:30:16: #1 total tags in treatment: 24199739 INFO @ Thu, 08 Oct 2020 20:30:16: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:30:16: #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 20:30:16: #1 tags after filtering in treatment: 24199739 INFO @ Thu, 08 Oct 2020 20:30:16: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:30:16: #1 finished! INFO @ Thu, 08 Oct 2020 20:30:16: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:30:16: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:30:18: #2 number of paired peaks: 322 WARNING @ Thu, 08 Oct 2020 20:30:18: Fewer paired peaks (322) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 322 pairs to build model! INFO @ Thu, 08 Oct 2020 20:30:18: start model_add_line... INFO @ Thu, 08 Oct 2020 20:30:18: start X-correlation... INFO @ Thu, 08 Oct 2020 20:30:18: end of X-cor INFO @ Thu, 08 Oct 2020 20:30:18: #2 finished! INFO @ Thu, 08 Oct 2020 20:30:18: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:30:18: #2 alternative fragment length(s) may be 1,11,598 bps INFO @ Thu, 08 Oct 2020 20:30:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6799193/SRX6799193.10_model.r WARNING @ Thu, 08 Oct 2020 20:30:18: #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 20:30:18: #2 You may need to consider one of the other alternative d(s): 1,11,598 WARNING @ Thu, 08 Oct 2020 20:30:18: #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 20:30:18: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:30:18: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:30:19: 20000000 INFO @ Thu, 08 Oct 2020 20:30:22: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:30:26: 21000000 INFO @ Thu, 08 Oct 2020 20:30:32: 22000000 INFO @ Thu, 08 Oct 2020 20:30:38: 23000000 INFO @ Thu, 08 Oct 2020 20:30:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6799193/SRX6799193.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:30:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6799193/SRX6799193.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:30:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6799193/SRX6799193.05_summits.bed INFO @ Thu, 08 Oct 2020 20:30:39: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:30:44: 24000000 INFO @ Thu, 08 Oct 2020 20:30:46: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:30:46: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:30:46: #1 total tags in treatment: 24199739 INFO @ Thu, 08 Oct 2020 20:30:46: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:30:46: #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 20:30:46: #1 tags after filtering in treatment: 24199739 INFO @ Thu, 08 Oct 2020 20:30:46: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:30:46: #1 finished! INFO @ Thu, 08 Oct 2020 20:30:46: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:30:46: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:30:48: #2 number of paired peaks: 322 WARNING @ Thu, 08 Oct 2020 20:30:48: Fewer paired peaks (322) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 322 pairs to build model! INFO @ Thu, 08 Oct 2020 20:30:48: start model_add_line... INFO @ Thu, 08 Oct 2020 20:30:48: start X-correlation... INFO @ Thu, 08 Oct 2020 20:30:48: end of X-cor INFO @ Thu, 08 Oct 2020 20:30:48: #2 finished! INFO @ Thu, 08 Oct 2020 20:30:48: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:30:48: #2 alternative fragment length(s) may be 1,11,598 bps INFO @ Thu, 08 Oct 2020 20:30:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6799193/SRX6799193.20_model.r WARNING @ Thu, 08 Oct 2020 20:30:48: #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 20:30:48: #2 You may need to consider one of the other alternative d(s): 1,11,598 WARNING @ Thu, 08 Oct 2020 20:30:48: #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 20:30:48: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:30:48: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:30:50: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:31:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6799193/SRX6799193.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:31:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6799193/SRX6799193.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:31:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6799193/SRX6799193.10_summits.bed INFO @ Thu, 08 Oct 2020 20:31:07: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:31:20: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:31:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6799193/SRX6799193.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:31:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6799193/SRX6799193.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:31:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6799193/SRX6799193.20_summits.bed INFO @ Thu, 08 Oct 2020 20:31:37: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling