Job ID = 6367581 SRX = SRX331337 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:34:35 prefetch.2.10.7: 1) Downloading 'SRR1030714'... 2020-06-15T23:34:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:38:43 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:38:43 prefetch.2.10.7: 1) 'SRR1030714' was downloaded successfully Read 20117538 spots for SRR1030714/SRR1030714.sra Written 20117538 spots for SRR1030714/SRR1030714.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: 00:04:31 20117538 reads; of these: 20117538 (100.00%) were unpaired; of these: 1021621 (5.08%) aligned 0 times 15666508 (77.87%) aligned exactly 1 time 3429409 (17.05%) aligned >1 times 94.92% overall alignment rate Time searching: 00:04:31 Overall time: 00:04:31 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] 2624149 / 19095917 = 0.1374 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 08:49:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331337/SRX331337.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331337/SRX331337.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331337/SRX331337.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331337/SRX331337.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 08:49:24: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:49:24: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:49:29: 1000000 INFO @ Tue, 16 Jun 2020 08:49:34: 2000000 INFO @ Tue, 16 Jun 2020 08:49:38: 3000000 INFO @ Tue, 16 Jun 2020 08:49:43: 4000000 INFO @ Tue, 16 Jun 2020 08:49:48: 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 @ Tue, 16 Jun 2020 08:49:53: 6000000 INFO @ Tue, 16 Jun 2020 08:49:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331337/SRX331337.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331337/SRX331337.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331337/SRX331337.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331337/SRX331337.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 08:49:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:49:54: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:49:58: 7000000 INFO @ Tue, 16 Jun 2020 08:49:59: 1000000 INFO @ Tue, 16 Jun 2020 08:50:03: 8000000 INFO @ Tue, 16 Jun 2020 08:50:04: 2000000 INFO @ Tue, 16 Jun 2020 08:50:08: 9000000 INFO @ Tue, 16 Jun 2020 08:50:09: 3000000 INFO @ Tue, 16 Jun 2020 08:50:13: 10000000 INFO @ Tue, 16 Jun 2020 08:50:14: 4000000 INFO @ Tue, 16 Jun 2020 08:50:18: 11000000 INFO @ Tue, 16 Jun 2020 08:50:19: 5000000 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 08:50:23: 12000000 INFO @ Tue, 16 Jun 2020 08:50:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331337/SRX331337.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331337/SRX331337.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331337/SRX331337.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331337/SRX331337.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 08:50:24: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:50:24: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:50:24: 6000000 INFO @ Tue, 16 Jun 2020 08:50:28: 13000000 INFO @ Tue, 16 Jun 2020 08:50:29: 7000000 INFO @ Tue, 16 Jun 2020 08:50:29: 1000000 INFO @ Tue, 16 Jun 2020 08:50:33: 14000000 INFO @ Tue, 16 Jun 2020 08:50:34: 2000000 INFO @ Tue, 16 Jun 2020 08:50:34: 8000000 INFO @ Tue, 16 Jun 2020 08:50:38: 15000000 INFO @ Tue, 16 Jun 2020 08:50:39: 9000000 INFO @ Tue, 16 Jun 2020 08:50:39: 3000000 INFO @ Tue, 16 Jun 2020 08:50:44: 16000000 INFO @ Tue, 16 Jun 2020 08:50:44: 4000000 INFO @ Tue, 16 Jun 2020 08:50:44: 10000000 INFO @ Tue, 16 Jun 2020 08:50:46: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:50:46: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:50:46: #1 total tags in treatment: 16471768 INFO @ Tue, 16 Jun 2020 08:50:46: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:50:46: #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 08:50:46: #1 tags after filtering in treatment: 16471768 INFO @ Tue, 16 Jun 2020 08:50:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:50:46: #1 finished! INFO @ Tue, 16 Jun 2020 08:50:46: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:50:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:50:47: #2 number of paired peaks: 243 WARNING @ Tue, 16 Jun 2020 08:50:47: Fewer paired peaks (243) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 243 pairs to build model! INFO @ Tue, 16 Jun 2020 08:50:47: start model_add_line... INFO @ Tue, 16 Jun 2020 08:50:48: start X-correlation... INFO @ Tue, 16 Jun 2020 08:50:48: end of X-cor INFO @ Tue, 16 Jun 2020 08:50:48: #2 finished! INFO @ Tue, 16 Jun 2020 08:50:48: #2 predicted fragment length is 46 bps INFO @ Tue, 16 Jun 2020 08:50:48: #2 alternative fragment length(s) may be 2,46 bps INFO @ Tue, 16 Jun 2020 08:50:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331337/SRX331337.05_model.r WARNING @ Tue, 16 Jun 2020 08:50:48: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:50:48: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Tue, 16 Jun 2020 08:50:48: #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 08:50:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:50:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:50:49: 5000000 INFO @ Tue, 16 Jun 2020 08:50:49: 11000000 INFO @ Tue, 16 Jun 2020 08:50:54: 6000000 INFO @ Tue, 16 Jun 2020 08:50:54: 12000000 INFO @ Tue, 16 Jun 2020 08:50:59: 7000000 INFO @ Tue, 16 Jun 2020 08:50:59: 13000000 INFO @ Tue, 16 Jun 2020 08:51:04: 8000000 INFO @ Tue, 16 Jun 2020 08:51:04: 14000000 INFO @ Tue, 16 Jun 2020 08:51:08: 9000000 INFO @ Tue, 16 Jun 2020 08:51:09: 15000000 INFO @ Tue, 16 Jun 2020 08:51:13: 10000000 INFO @ Tue, 16 Jun 2020 08:51:14: 16000000 INFO @ Tue, 16 Jun 2020 08:51:17: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:51:17: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:51:17: #1 total tags in treatment: 16471768 INFO @ Tue, 16 Jun 2020 08:51:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:51:17: #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 08:51:17: #1 tags after filtering in treatment: 16471768 INFO @ Tue, 16 Jun 2020 08:51:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:51:17: #1 finished! INFO @ Tue, 16 Jun 2020 08:51:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:51:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:51:18: #2 number of paired peaks: 243 WARNING @ Tue, 16 Jun 2020 08:51:18: Fewer paired peaks (243) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 243 pairs to build model! INFO @ Tue, 16 Jun 2020 08:51:18: start model_add_line... INFO @ Tue, 16 Jun 2020 08:51:18: start X-correlation... INFO @ Tue, 16 Jun 2020 08:51:18: end of X-cor INFO @ Tue, 16 Jun 2020 08:51:18: #2 finished! INFO @ Tue, 16 Jun 2020 08:51:18: #2 predicted fragment length is 46 bps INFO @ Tue, 16 Jun 2020 08:51:18: #2 alternative fragment length(s) may be 2,46 bps INFO @ Tue, 16 Jun 2020 08:51:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331337/SRX331337.10_model.r WARNING @ Tue, 16 Jun 2020 08:51:18: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:51:18: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Tue, 16 Jun 2020 08:51:18: #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 08:51:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:51:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:51:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:51:18: 11000000 INFO @ Tue, 16 Jun 2020 08:51:23: 12000000 INFO @ Tue, 16 Jun 2020 08:51:28: 13000000 INFO @ Tue, 16 Jun 2020 08:51:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331337/SRX331337.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:51:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331337/SRX331337.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:51:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331337/SRX331337.05_summits.bed INFO @ Tue, 16 Jun 2020 08:51:32: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (672 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:51:33: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:51:38: 15000000 INFO @ Tue, 16 Jun 2020 08:51:43: 16000000 INFO @ Tue, 16 Jun 2020 08:51:45: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:51:45: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:51:45: #1 total tags in treatment: 16471768 INFO @ Tue, 16 Jun 2020 08:51:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:51:45: #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 08:51:46: #1 tags after filtering in treatment: 16471768 INFO @ Tue, 16 Jun 2020 08:51:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:51:46: #1 finished! INFO @ Tue, 16 Jun 2020 08:51:46: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:51:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:51:47: #2 number of paired peaks: 243 WARNING @ Tue, 16 Jun 2020 08:51:47: Fewer paired peaks (243) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 243 pairs to build model! INFO @ Tue, 16 Jun 2020 08:51:47: start model_add_line... INFO @ Tue, 16 Jun 2020 08:51:47: start X-correlation... INFO @ Tue, 16 Jun 2020 08:51:47: end of X-cor INFO @ Tue, 16 Jun 2020 08:51:47: #2 finished! INFO @ Tue, 16 Jun 2020 08:51:47: #2 predicted fragment length is 46 bps INFO @ Tue, 16 Jun 2020 08:51:47: #2 alternative fragment length(s) may be 2,46 bps INFO @ Tue, 16 Jun 2020 08:51:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331337/SRX331337.20_model.r WARNING @ Tue, 16 Jun 2020 08:51:47: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:51:47: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Tue, 16 Jun 2020 08:51:47: #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 08:51:47: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:51:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:51:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:52:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331337/SRX331337.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:52:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331337/SRX331337.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:52:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331337/SRX331337.10_summits.bed INFO @ Tue, 16 Jun 2020 08:52:02: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (422 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:52:17: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:52:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331337/SRX331337.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:52:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331337/SRX331337.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:52:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331337/SRX331337.20_summits.bed INFO @ Tue, 16 Jun 2020 08:52:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (154 records, 4 fields): 1 millis CompletedMACS2peakCalling