Job ID = 6367603 SRX = SRX331359 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:32:20 prefetch.2.10.7: 1) Downloading 'SRR947596'... 2020-06-15T23:32:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:36:24 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:36:24 prefetch.2.10.7: 1) 'SRR947596' was downloaded successfully Read 21145599 spots for SRR947596/SRR947596.sra Written 21145599 spots for SRR947596/SRR947596.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: 00:04:40 21145599 reads; of these: 21145599 (100.00%) were unpaired; of these: 2101872 (9.94%) aligned 0 times 15701872 (74.26%) aligned exactly 1 time 3341855 (15.80%) aligned >1 times 90.06% overall alignment rate Time searching: 00:04:40 Overall time: 00:04:40 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] 8890967 / 19043727 = 0.4669 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 08:46:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331359/SRX331359.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331359/SRX331359.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331359/SRX331359.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331359/SRX331359.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 08:46:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:46:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:46:42: 1000000 INFO @ Tue, 16 Jun 2020 08:46:47: 2000000 INFO @ Tue, 16 Jun 2020 08:46:52: 3000000 INFO @ Tue, 16 Jun 2020 08:46:57: 4000000 INFO @ Tue, 16 Jun 2020 08:47:02: 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 08:47:07: 6000000 INFO @ Tue, 16 Jun 2020 08:47:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331359/SRX331359.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331359/SRX331359.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331359/SRX331359.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331359/SRX331359.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 08:47:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:47:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:47:11: 7000000 INFO @ Tue, 16 Jun 2020 08:47:13: 1000000 INFO @ Tue, 16 Jun 2020 08:47:17: 8000000 INFO @ Tue, 16 Jun 2020 08:47:19: 2000000 INFO @ Tue, 16 Jun 2020 08:47:21: 9000000 INFO @ Tue, 16 Jun 2020 08:47:24: 3000000 INFO @ Tue, 16 Jun 2020 08:47:26: 10000000 INFO @ Tue, 16 Jun 2020 08:47:27: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:47:27: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:47:27: #1 total tags in treatment: 10152760 INFO @ Tue, 16 Jun 2020 08:47:27: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:47:27: #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 08:47:27: #1 tags after filtering in treatment: 10152760 INFO @ Tue, 16 Jun 2020 08:47:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:47:27: #1 finished! INFO @ Tue, 16 Jun 2020 08:47:27: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:47:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:47:28: #2 number of paired peaks: 472 WARNING @ Tue, 16 Jun 2020 08:47:28: Fewer paired peaks (472) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 472 pairs to build model! INFO @ Tue, 16 Jun 2020 08:47:28: start model_add_line... INFO @ Tue, 16 Jun 2020 08:47:28: start X-correlation... INFO @ Tue, 16 Jun 2020 08:47:28: end of X-cor INFO @ Tue, 16 Jun 2020 08:47:28: #2 finished! INFO @ Tue, 16 Jun 2020 08:47:28: #2 predicted fragment length is 46 bps INFO @ Tue, 16 Jun 2020 08:47:28: #2 alternative fragment length(s) may be 2,46 bps INFO @ Tue, 16 Jun 2020 08:47:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331359/SRX331359.05_model.r WARNING @ Tue, 16 Jun 2020 08:47:28: #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 08:47:28: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Tue, 16 Jun 2020 08:47:28: #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 08:47:28: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:47:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:47:29: 4000000 INFO @ Tue, 16 Jun 2020 08:47:35: 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 08:47:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331359/SRX331359.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331359/SRX331359.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331359/SRX331359.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331359/SRX331359.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 08:47:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:47:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:47:40: 6000000 INFO @ Tue, 16 Jun 2020 08:47:43: 1000000 INFO @ Tue, 16 Jun 2020 08:47:46: 7000000 INFO @ Tue, 16 Jun 2020 08:47:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:47:49: 2000000 INFO @ Tue, 16 Jun 2020 08:47:51: 8000000 INFO @ Tue, 16 Jun 2020 08:47:54: 3000000 INFO @ Tue, 16 Jun 2020 08:47:57: 9000000 INFO @ Tue, 16 Jun 2020 08:47:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331359/SRX331359.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:47:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331359/SRX331359.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:47:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331359/SRX331359.05_summits.bed INFO @ Tue, 16 Jun 2020 08:47:58: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (797 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:48:00: 4000000 INFO @ Tue, 16 Jun 2020 08:48:02: 10000000 INFO @ Tue, 16 Jun 2020 08:48:03: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:48:03: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:48:03: #1 total tags in treatment: 10152760 INFO @ Tue, 16 Jun 2020 08:48:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:48:03: #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 08:48:03: #1 tags after filtering in treatment: 10152760 INFO @ Tue, 16 Jun 2020 08:48:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:48:03: #1 finished! INFO @ Tue, 16 Jun 2020 08:48:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:48:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:48:04: #2 number of paired peaks: 472 WARNING @ Tue, 16 Jun 2020 08:48:04: Fewer paired peaks (472) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 472 pairs to build model! INFO @ Tue, 16 Jun 2020 08:48:04: start model_add_line... INFO @ Tue, 16 Jun 2020 08:48:04: start X-correlation... INFO @ Tue, 16 Jun 2020 08:48:04: end of X-cor INFO @ Tue, 16 Jun 2020 08:48:04: #2 finished! INFO @ Tue, 16 Jun 2020 08:48:04: #2 predicted fragment length is 46 bps INFO @ Tue, 16 Jun 2020 08:48:04: #2 alternative fragment length(s) may be 2,46 bps INFO @ Tue, 16 Jun 2020 08:48:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331359/SRX331359.10_model.r WARNING @ Tue, 16 Jun 2020 08:48:04: #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 08:48:04: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Tue, 16 Jun 2020 08:48:04: #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 08:48:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:48:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:48:05: 5000000 INFO @ Tue, 16 Jun 2020 08:48:10: 6000000 INFO @ Tue, 16 Jun 2020 08:48:15: 7000000 INFO @ Tue, 16 Jun 2020 08:48:21: 8000000 INFO @ Tue, 16 Jun 2020 08:48:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:48:26: 9000000 INFO @ Tue, 16 Jun 2020 08:48:31: 10000000 INFO @ Tue, 16 Jun 2020 08:48:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331359/SRX331359.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:48:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331359/SRX331359.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:48:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331359/SRX331359.10_summits.bed INFO @ Tue, 16 Jun 2020 08:48:32: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (570 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:48:32: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:48:32: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:48:32: #1 total tags in treatment: 10152760 INFO @ Tue, 16 Jun 2020 08:48:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:48:32: #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 08:48:32: #1 tags after filtering in treatment: 10152760 INFO @ Tue, 16 Jun 2020 08:48:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:48:32: #1 finished! INFO @ Tue, 16 Jun 2020 08:48:32: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:48:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:48:33: #2 number of paired peaks: 472 WARNING @ Tue, 16 Jun 2020 08:48:33: Fewer paired peaks (472) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 472 pairs to build model! INFO @ Tue, 16 Jun 2020 08:48:33: start model_add_line... INFO @ Tue, 16 Jun 2020 08:48:33: start X-correlation... INFO @ Tue, 16 Jun 2020 08:48:33: end of X-cor INFO @ Tue, 16 Jun 2020 08:48:33: #2 finished! INFO @ Tue, 16 Jun 2020 08:48:33: #2 predicted fragment length is 46 bps INFO @ Tue, 16 Jun 2020 08:48:33: #2 alternative fragment length(s) may be 2,46 bps INFO @ Tue, 16 Jun 2020 08:48:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331359/SRX331359.20_model.r WARNING @ Tue, 16 Jun 2020 08:48:33: #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 08:48:33: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Tue, 16 Jun 2020 08:48:33: #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 08:48:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:48:33: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:48:52: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:49:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331359/SRX331359.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:49:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331359/SRX331359.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:49:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331359/SRX331359.20_summits.bed INFO @ Tue, 16 Jun 2020 08:49:02: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (230 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。