Job ID = 6366650 SRX = SRX2163951 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:59:08 prefetch.2.10.7: 1) Downloading 'SRR4242866'... 2020-06-15T22:59:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:04:21 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:04:21 prefetch.2.10.7: 1) 'SRR4242866' was downloaded successfully Read 45999734 spots for SRR4242866/SRR4242866.sra Written 45999734 spots for SRR4242866/SRR4242866.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: 00:13:44 45999734 reads; of these: 45999734 (100.00%) were unpaired; of these: 21172535 (46.03%) aligned 0 times 20948089 (45.54%) aligned exactly 1 time 3879110 (8.43%) aligned >1 times 53.97% overall alignment rate Time searching: 00:13:44 Overall time: 00:13:44 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] 11215813 / 24827199 = 0.4518 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 08:30:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2163951/SRX2163951.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2163951/SRX2163951.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2163951/SRX2163951.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2163951/SRX2163951.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 08:30:23: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:30:23: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:30:31: 1000000 INFO @ Tue, 16 Jun 2020 08:30:39: 2000000 INFO @ Tue, 16 Jun 2020 08:30:46: 3000000 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 08:30:53: 4000000 INFO @ Tue, 16 Jun 2020 08:30:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2163951/SRX2163951.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2163951/SRX2163951.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2163951/SRX2163951.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2163951/SRX2163951.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 08:30:53: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:30:53: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:31:02: 5000000 INFO @ Tue, 16 Jun 2020 08:31:02: 1000000 INFO @ Tue, 16 Jun 2020 08:31:10: 6000000 INFO @ Tue, 16 Jun 2020 08:31:10: 2000000 INFO @ Tue, 16 Jun 2020 08:31:18: 7000000 INFO @ Tue, 16 Jun 2020 08:31:19: 3000000 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 08:31:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2163951/SRX2163951.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2163951/SRX2163951.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2163951/SRX2163951.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2163951/SRX2163951.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 08:31:23: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:31:23: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:31:26: 8000000 INFO @ Tue, 16 Jun 2020 08:31:27: 4000000 INFO @ Tue, 16 Jun 2020 08:31:33: 1000000 INFO @ Tue, 16 Jun 2020 08:31:35: 9000000 INFO @ Tue, 16 Jun 2020 08:31:35: 5000000 INFO @ Tue, 16 Jun 2020 08:31:42: 2000000 INFO @ Tue, 16 Jun 2020 08:31:43: 10000000 INFO @ Tue, 16 Jun 2020 08:31:44: 6000000 INFO @ Tue, 16 Jun 2020 08:31:50: 3000000 INFO @ Tue, 16 Jun 2020 08:31:51: 11000000 INFO @ Tue, 16 Jun 2020 08:31:52: 7000000 INFO @ Tue, 16 Jun 2020 08:31:59: 4000000 INFO @ Tue, 16 Jun 2020 08:31:59: 12000000 INFO @ Tue, 16 Jun 2020 08:32:00: 8000000 INFO @ Tue, 16 Jun 2020 08:32:07: 5000000 INFO @ Tue, 16 Jun 2020 08:32:08: 13000000 INFO @ Tue, 16 Jun 2020 08:32:08: 9000000 INFO @ Tue, 16 Jun 2020 08:32:13: #1 tag size is determined as 92 bps INFO @ Tue, 16 Jun 2020 08:32:13: #1 tag size = 92 INFO @ Tue, 16 Jun 2020 08:32:13: #1 total tags in treatment: 13611386 INFO @ Tue, 16 Jun 2020 08:32:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:32:13: #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 08:32:13: #1 tags after filtering in treatment: 13611386 INFO @ Tue, 16 Jun 2020 08:32:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:32:13: #1 finished! INFO @ Tue, 16 Jun 2020 08:32:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:32:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:32:14: #2 number of paired peaks: 333 WARNING @ Tue, 16 Jun 2020 08:32:14: Fewer paired peaks (333) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 333 pairs to build model! INFO @ Tue, 16 Jun 2020 08:32:14: start model_add_line... INFO @ Tue, 16 Jun 2020 08:32:14: start X-correlation... INFO @ Tue, 16 Jun 2020 08:32:14: end of X-cor INFO @ Tue, 16 Jun 2020 08:32:14: #2 finished! INFO @ Tue, 16 Jun 2020 08:32:14: #2 predicted fragment length is 88 bps INFO @ Tue, 16 Jun 2020 08:32:14: #2 alternative fragment length(s) may be 4,88 bps INFO @ Tue, 16 Jun 2020 08:32:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2163951/SRX2163951.05_model.r WARNING @ Tue, 16 Jun 2020 08:32:14: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:32:14: #2 You may need to consider one of the other alternative d(s): 4,88 WARNING @ Tue, 16 Jun 2020 08:32:14: #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 08:32:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:32:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:32:15: 6000000 INFO @ Tue, 16 Jun 2020 08:32:17: 10000000 INFO @ Tue, 16 Jun 2020 08:32:24: 7000000 INFO @ Tue, 16 Jun 2020 08:32:25: 11000000 INFO @ Tue, 16 Jun 2020 08:32:32: 8000000 INFO @ Tue, 16 Jun 2020 08:32:33: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:32:40: 9000000 INFO @ Tue, 16 Jun 2020 08:32:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:32:41: 13000000 INFO @ Tue, 16 Jun 2020 08:32:47: #1 tag size is determined as 92 bps INFO @ Tue, 16 Jun 2020 08:32:47: #1 tag size = 92 INFO @ Tue, 16 Jun 2020 08:32:47: #1 total tags in treatment: 13611386 INFO @ Tue, 16 Jun 2020 08:32:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:32:47: #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 08:32:47: #1 tags after filtering in treatment: 13611386 INFO @ Tue, 16 Jun 2020 08:32:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:32:47: #1 finished! INFO @ Tue, 16 Jun 2020 08:32:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:32:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:32:48: #2 number of paired peaks: 333 WARNING @ Tue, 16 Jun 2020 08:32:48: Fewer paired peaks (333) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 333 pairs to build model! INFO @ Tue, 16 Jun 2020 08:32:48: start model_add_line... INFO @ Tue, 16 Jun 2020 08:32:48: start X-correlation... INFO @ Tue, 16 Jun 2020 08:32:48: end of X-cor INFO @ Tue, 16 Jun 2020 08:32:48: #2 finished! INFO @ Tue, 16 Jun 2020 08:32:48: #2 predicted fragment length is 88 bps INFO @ Tue, 16 Jun 2020 08:32:48: #2 alternative fragment length(s) may be 4,88 bps INFO @ Tue, 16 Jun 2020 08:32:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2163951/SRX2163951.10_model.r WARNING @ Tue, 16 Jun 2020 08:32:48: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:32:48: #2 You may need to consider one of the other alternative d(s): 4,88 WARNING @ Tue, 16 Jun 2020 08:32:48: #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 08:32:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:32:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:32:49: 10000000 INFO @ Tue, 16 Jun 2020 08:32:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2163951/SRX2163951.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:32:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2163951/SRX2163951.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:32:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2163951/SRX2163951.05_summits.bed INFO @ Tue, 16 Jun 2020 08:32:53: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (627 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:32:56: 11000000 INFO @ Tue, 16 Jun 2020 08:33:03: 12000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:33:11: 13000000 INFO @ Tue, 16 Jun 2020 08:33:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:33:15: #1 tag size is determined as 92 bps INFO @ Tue, 16 Jun 2020 08:33:15: #1 tag size = 92 INFO @ Tue, 16 Jun 2020 08:33:15: #1 total tags in treatment: 13611386 INFO @ Tue, 16 Jun 2020 08:33:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:33:15: #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 08:33:15: #1 tags after filtering in treatment: 13611386 INFO @ Tue, 16 Jun 2020 08:33:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:33:15: #1 finished! INFO @ Tue, 16 Jun 2020 08:33:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:33:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:33:16: #2 number of paired peaks: 333 WARNING @ Tue, 16 Jun 2020 08:33:16: Fewer paired peaks (333) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 333 pairs to build model! INFO @ Tue, 16 Jun 2020 08:33:16: start model_add_line... INFO @ Tue, 16 Jun 2020 08:33:16: start X-correlation... INFO @ Tue, 16 Jun 2020 08:33:16: end of X-cor INFO @ Tue, 16 Jun 2020 08:33:16: #2 finished! INFO @ Tue, 16 Jun 2020 08:33:16: #2 predicted fragment length is 88 bps INFO @ Tue, 16 Jun 2020 08:33:16: #2 alternative fragment length(s) may be 4,88 bps INFO @ Tue, 16 Jun 2020 08:33:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2163951/SRX2163951.20_model.r WARNING @ Tue, 16 Jun 2020 08:33:16: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:33:16: #2 You may need to consider one of the other alternative d(s): 4,88 WARNING @ Tue, 16 Jun 2020 08:33:16: #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 08:33:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:33:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:33:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2163951/SRX2163951.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:33:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2163951/SRX2163951.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:33:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2163951/SRX2163951.10_summits.bed INFO @ Tue, 16 Jun 2020 08:33:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (441 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:33:43: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:33:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2163951/SRX2163951.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:33:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2163951/SRX2163951.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:33:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2163951/SRX2163951.20_summits.bed INFO @ Tue, 16 Jun 2020 08:33:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (256 records, 4 fields): 1 millis CompletedMACS2peakCalling