Job ID = 6366049 SRX = SRX059221 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:30:14 prefetch.2.10.7: 1) Downloading 'SRR190661'... 2020-06-15T22:30:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:32:14 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:32:14 prefetch.2.10.7: 1) 'SRR190661' was downloaded successfully Read 19874451 spots for SRR190661/SRR190661.sra Written 19874451 spots for SRR190661/SRR190661.sra 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: 00:03:52 19874451 reads; of these: 19874451 (100.00%) were unpaired; of these: 311424 (1.57%) aligned 0 times 16205456 (81.54%) aligned exactly 1 time 3357571 (16.89%) aligned >1 times 98.43% overall alignment rate Time searching: 00:03:52 Overall time: 00:03:52 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 8 files... [bam_rmdupse_core] 2055445 / 19563027 = 0.1051 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 @ Tue, 16 Jun 2020 07:42:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059221/SRX059221.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059221/SRX059221.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059221/SRX059221.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059221/SRX059221.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 @ Tue, 16 Jun 2020 07:42:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:42:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:42:38: 1000000 INFO @ Tue, 16 Jun 2020 07:42:44: 2000000 INFO @ Tue, 16 Jun 2020 07:42:50: 3000000 INFO @ Tue, 16 Jun 2020 07:42:56: 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 @ Tue, 16 Jun 2020 07:43:02: 5000000 INFO @ Tue, 16 Jun 2020 07:43:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059221/SRX059221.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059221/SRX059221.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059221/SRX059221.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059221/SRX059221.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 @ Tue, 16 Jun 2020 07:43:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:43:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:43:08: 6000000 INFO @ Tue, 16 Jun 2020 07:43:09: 1000000 INFO @ Tue, 16 Jun 2020 07:43:15: 7000000 INFO @ Tue, 16 Jun 2020 07:43:16: 2000000 INFO @ Tue, 16 Jun 2020 07:43:22: 8000000 INFO @ Tue, 16 Jun 2020 07:43:23: 3000000 INFO @ Tue, 16 Jun 2020 07:43:29: 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 @ Tue, 16 Jun 2020 07:43:31: 4000000 INFO @ Tue, 16 Jun 2020 07:43:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059221/SRX059221.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059221/SRX059221.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059221/SRX059221.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059221/SRX059221.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 @ Tue, 16 Jun 2020 07:43:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:43:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:43:36: 10000000 INFO @ Tue, 16 Jun 2020 07:43:38: 5000000 INFO @ Tue, 16 Jun 2020 07:43:39: 1000000 INFO @ Tue, 16 Jun 2020 07:43:42: 11000000 INFO @ Tue, 16 Jun 2020 07:43:45: 6000000 INFO @ Tue, 16 Jun 2020 07:43:46: 2000000 INFO @ Tue, 16 Jun 2020 07:43:49: 12000000 INFO @ Tue, 16 Jun 2020 07:43:52: 7000000 INFO @ Tue, 16 Jun 2020 07:43:53: 3000000 INFO @ Tue, 16 Jun 2020 07:43:56: 13000000 INFO @ Tue, 16 Jun 2020 07:44:00: 8000000 INFO @ Tue, 16 Jun 2020 07:44:00: 4000000 INFO @ Tue, 16 Jun 2020 07:44:03: 14000000 INFO @ Tue, 16 Jun 2020 07:44:07: 5000000 INFO @ Tue, 16 Jun 2020 07:44:07: 9000000 INFO @ Tue, 16 Jun 2020 07:44:10: 15000000 INFO @ Tue, 16 Jun 2020 07:44:14: 6000000 INFO @ Tue, 16 Jun 2020 07:44:14: 10000000 INFO @ Tue, 16 Jun 2020 07:44:17: 16000000 INFO @ Tue, 16 Jun 2020 07:44:21: 7000000 INFO @ Tue, 16 Jun 2020 07:44:22: 11000000 INFO @ Tue, 16 Jun 2020 07:44:24: 17000000 INFO @ Tue, 16 Jun 2020 07:44:27: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 07:44:27: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 07:44:27: #1 total tags in treatment: 17507582 INFO @ Tue, 16 Jun 2020 07:44:27: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:44:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 07:44:27: 8000000 INFO @ Tue, 16 Jun 2020 07:44:28: #1 tags after filtering in treatment: 17507582 INFO @ Tue, 16 Jun 2020 07:44:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:44:28: #1 finished! INFO @ Tue, 16 Jun 2020 07:44:28: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:44:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:44:29: 12000000 INFO @ Tue, 16 Jun 2020 07:44:29: #2 number of paired peaks: 166 WARNING @ Tue, 16 Jun 2020 07:44:29: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Tue, 16 Jun 2020 07:44:29: start model_add_line... INFO @ Tue, 16 Jun 2020 07:44:29: start X-correlation... INFO @ Tue, 16 Jun 2020 07:44:29: end of X-cor INFO @ Tue, 16 Jun 2020 07:44:29: #2 finished! INFO @ Tue, 16 Jun 2020 07:44:29: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 07:44:29: #2 alternative fragment length(s) may be 1,26,497,506,511,515,518,533 bps INFO @ Tue, 16 Jun 2020 07:44:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059221/SRX059221.05_model.r WARNING @ Tue, 16 Jun 2020 07:44:29: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:44:29: #2 You may need to consider one of the other alternative d(s): 1,26,497,506,511,515,518,533 WARNING @ Tue, 16 Jun 2020 07:44:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 07:44:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:44:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:44:34: 9000000 INFO @ Tue, 16 Jun 2020 07:44:36: 13000000 INFO @ Tue, 16 Jun 2020 07:44:41: 10000000 INFO @ Tue, 16 Jun 2020 07:44:43: 14000000 INFO @ Tue, 16 Jun 2020 07:44:48: 11000000 INFO @ Tue, 16 Jun 2020 07:44:50: 15000000 INFO @ Tue, 16 Jun 2020 07:44:54: 12000000 INFO @ Tue, 16 Jun 2020 07:44:58: 16000000 INFO @ Tue, 16 Jun 2020 07:44:59: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:45:01: 13000000 INFO @ Tue, 16 Jun 2020 07:45:05: 17000000 INFO @ Tue, 16 Jun 2020 07:45:08: 14000000 INFO @ Tue, 16 Jun 2020 07:45:09: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 07:45:09: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 07:45:09: #1 total tags in treatment: 17507582 INFO @ Tue, 16 Jun 2020 07:45:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:45:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 07:45:09: #1 tags after filtering in treatment: 17507582 INFO @ Tue, 16 Jun 2020 07:45:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:45:09: #1 finished! INFO @ Tue, 16 Jun 2020 07:45:09: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:45:09: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:45:10: #2 number of paired peaks: 166 WARNING @ Tue, 16 Jun 2020 07:45:10: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Tue, 16 Jun 2020 07:45:10: start model_add_line... INFO @ Tue, 16 Jun 2020 07:45:10: start X-correlation... INFO @ Tue, 16 Jun 2020 07:45:11: end of X-cor INFO @ Tue, 16 Jun 2020 07:45:11: #2 finished! INFO @ Tue, 16 Jun 2020 07:45:11: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 07:45:11: #2 alternative fragment length(s) may be 1,26,497,506,511,515,518,533 bps INFO @ Tue, 16 Jun 2020 07:45:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059221/SRX059221.10_model.r WARNING @ Tue, 16 Jun 2020 07:45:11: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:45:11: #2 You may need to consider one of the other alternative d(s): 1,26,497,506,511,515,518,533 WARNING @ Tue, 16 Jun 2020 07:45:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 07:45:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:45:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:45:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059221/SRX059221.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:45:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059221/SRX059221.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:45:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059221/SRX059221.05_summits.bed INFO @ Tue, 16 Jun 2020 07:45:14: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:45:14: 15000000 INFO @ Tue, 16 Jun 2020 07:45:21: 16000000 INFO @ Tue, 16 Jun 2020 07:45:27: 17000000 INFO @ Tue, 16 Jun 2020 07:45:30: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 07:45:30: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 07:45:30: #1 total tags in treatment: 17507582 INFO @ Tue, 16 Jun 2020 07:45:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:45:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 07:45:31: #1 tags after filtering in treatment: 17507582 INFO @ Tue, 16 Jun 2020 07:45:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:45:31: #1 finished! INFO @ Tue, 16 Jun 2020 07:45:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:45:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:45:32: #2 number of paired peaks: 166 WARNING @ Tue, 16 Jun 2020 07:45:32: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Tue, 16 Jun 2020 07:45:32: start model_add_line... INFO @ Tue, 16 Jun 2020 07:45:32: start X-correlation... INFO @ Tue, 16 Jun 2020 07:45:32: end of X-cor INFO @ Tue, 16 Jun 2020 07:45:32: #2 finished! INFO @ Tue, 16 Jun 2020 07:45:32: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 07:45:32: #2 alternative fragment length(s) may be 1,26,497,506,511,515,518,533 bps INFO @ Tue, 16 Jun 2020 07:45:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059221/SRX059221.20_model.r WARNING @ Tue, 16 Jun 2020 07:45:32: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:45:32: #2 You may need to consider one of the other alternative d(s): 1,26,497,506,511,515,518,533 WARNING @ Tue, 16 Jun 2020 07:45:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 07:45:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:45:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:45:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:45:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059221/SRX059221.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:45:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059221/SRX059221.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:45:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059221/SRX059221.10_summits.bed INFO @ Tue, 16 Jun 2020 07:45:54: Done! BigWig に変換しました。 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:46:03: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:46:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059221/SRX059221.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:46:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059221/SRX059221.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:46:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059221/SRX059221.20_summits.bed INFO @ Tue, 16 Jun 2020 07:46:17: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling