Job ID = 6366987 SRX = SRX257686 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:35:50 prefetch.2.10.7: 1) Downloading 'SRR800702'... 2020-06-15T23:35:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:45:28 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:45:28 prefetch.2.10.7: 1) 'SRR800702' was downloaded successfully Read 23010900 spots for SRR800702/SRR800702.sra Written 23010900 spots for SRR800702/SRR800702.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:48 23010900 reads; of these: 23010900 (100.00%) were unpaired; of these: 1927320 (8.38%) aligned 0 times 17588115 (76.43%) aligned exactly 1 time 3495465 (15.19%) aligned >1 times 91.62% overall alignment rate Time searching: 00:03:49 Overall time: 00:03:49 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] 4390765 / 21083580 = 0.2083 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 08:55:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257686/SRX257686.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257686/SRX257686.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257686/SRX257686.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257686/SRX257686.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 08:55:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:55:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:55:24: 1000000 INFO @ Tue, 16 Jun 2020 08:55:29: 2000000 INFO @ Tue, 16 Jun 2020 08:55:35: 3000000 INFO @ Tue, 16 Jun 2020 08:55:40: 4000000 INFO @ Tue, 16 Jun 2020 08:55:45: 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 08:55:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257686/SRX257686.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257686/SRX257686.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257686/SRX257686.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257686/SRX257686.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 08:55:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:55:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:55:51: 6000000 INFO @ Tue, 16 Jun 2020 08:55:54: 1000000 INFO @ Tue, 16 Jun 2020 08:55:57: 7000000 INFO @ Tue, 16 Jun 2020 08:56:00: 2000000 INFO @ Tue, 16 Jun 2020 08:56:02: 8000000 INFO @ Tue, 16 Jun 2020 08:56:05: 3000000 INFO @ Tue, 16 Jun 2020 08:56:08: 9000000 INFO @ Tue, 16 Jun 2020 08:56:11: 4000000 INFO @ Tue, 16 Jun 2020 08:56:13: 10000000 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 08:56:17: 5000000 INFO @ Tue, 16 Jun 2020 08:56:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257686/SRX257686.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257686/SRX257686.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257686/SRX257686.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257686/SRX257686.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 08:56:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:56:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:56:19: 11000000 INFO @ Tue, 16 Jun 2020 08:56:23: 6000000 INFO @ Tue, 16 Jun 2020 08:56:24: 1000000 INFO @ Tue, 16 Jun 2020 08:56:25: 12000000 INFO @ Tue, 16 Jun 2020 08:56:28: 7000000 INFO @ Tue, 16 Jun 2020 08:56:29: 2000000 INFO @ Tue, 16 Jun 2020 08:56:30: 13000000 INFO @ Tue, 16 Jun 2020 08:56:34: 8000000 INFO @ Tue, 16 Jun 2020 08:56:34: 3000000 INFO @ Tue, 16 Jun 2020 08:56:36: 14000000 INFO @ Tue, 16 Jun 2020 08:56:39: 4000000 INFO @ Tue, 16 Jun 2020 08:56:40: 9000000 INFO @ Tue, 16 Jun 2020 08:56:42: 15000000 INFO @ Tue, 16 Jun 2020 08:56:45: 5000000 INFO @ Tue, 16 Jun 2020 08:56:46: 10000000 INFO @ Tue, 16 Jun 2020 08:56:47: 16000000 INFO @ Tue, 16 Jun 2020 08:56:50: 6000000 INFO @ Tue, 16 Jun 2020 08:56:51: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:56:51: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:56:51: #1 total tags in treatment: 16692815 INFO @ Tue, 16 Jun 2020 08:56:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:56:51: #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 08:56:51: #1 tags after filtering in treatment: 16692815 INFO @ Tue, 16 Jun 2020 08:56:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:56:51: #1 finished! INFO @ Tue, 16 Jun 2020 08:56:51: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:56:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:56:51: 11000000 INFO @ Tue, 16 Jun 2020 08:56:53: #2 number of paired peaks: 290 WARNING @ Tue, 16 Jun 2020 08:56:53: Fewer paired peaks (290) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 290 pairs to build model! INFO @ Tue, 16 Jun 2020 08:56:53: start model_add_line... INFO @ Tue, 16 Jun 2020 08:56:53: start X-correlation... INFO @ Tue, 16 Jun 2020 08:56:53: end of X-cor INFO @ Tue, 16 Jun 2020 08:56:53: #2 finished! INFO @ Tue, 16 Jun 2020 08:56:53: #2 predicted fragment length is 43 bps INFO @ Tue, 16 Jun 2020 08:56:53: #2 alternative fragment length(s) may be 1,43,571 bps INFO @ Tue, 16 Jun 2020 08:56:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257686/SRX257686.05_model.r WARNING @ Tue, 16 Jun 2020 08:56:53: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:56:53: #2 You may need to consider one of the other alternative d(s): 1,43,571 WARNING @ Tue, 16 Jun 2020 08:56:53: #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 08:56:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:56:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:56:55: 7000000 INFO @ Tue, 16 Jun 2020 08:56:57: 12000000 INFO @ Tue, 16 Jun 2020 08:57:00: 8000000 INFO @ Tue, 16 Jun 2020 08:57:03: 13000000 INFO @ Tue, 16 Jun 2020 08:57:05: 9000000 INFO @ Tue, 16 Jun 2020 08:57:09: 14000000 INFO @ Tue, 16 Jun 2020 08:57:10: 10000000 INFO @ Tue, 16 Jun 2020 08:57:15: 15000000 INFO @ Tue, 16 Jun 2020 08:57:15: 11000000 INFO @ Tue, 16 Jun 2020 08:57:20: 16000000 INFO @ Tue, 16 Jun 2020 08:57:21: 12000000 INFO @ Tue, 16 Jun 2020 08:57:22: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:57:24: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:57:24: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:57:24: #1 total tags in treatment: 16692815 INFO @ Tue, 16 Jun 2020 08:57:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:57:24: #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 08:57:25: #1 tags after filtering in treatment: 16692815 INFO @ Tue, 16 Jun 2020 08:57:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:57:25: #1 finished! INFO @ Tue, 16 Jun 2020 08:57:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:57:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:57:26: 13000000 INFO @ Tue, 16 Jun 2020 08:57:26: #2 number of paired peaks: 290 WARNING @ Tue, 16 Jun 2020 08:57:26: Fewer paired peaks (290) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 290 pairs to build model! INFO @ Tue, 16 Jun 2020 08:57:26: start model_add_line... INFO @ Tue, 16 Jun 2020 08:57:26: start X-correlation... INFO @ Tue, 16 Jun 2020 08:57:26: end of X-cor INFO @ Tue, 16 Jun 2020 08:57:26: #2 finished! INFO @ Tue, 16 Jun 2020 08:57:26: #2 predicted fragment length is 43 bps INFO @ Tue, 16 Jun 2020 08:57:26: #2 alternative fragment length(s) may be 1,43,571 bps INFO @ Tue, 16 Jun 2020 08:57:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257686/SRX257686.10_model.r WARNING @ Tue, 16 Jun 2020 08:57:26: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:57:26: #2 You may need to consider one of the other alternative d(s): 1,43,571 WARNING @ Tue, 16 Jun 2020 08:57:26: #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 08:57:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:57:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:57:31: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:57:35: 15000000 INFO @ Tue, 16 Jun 2020 08:57:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257686/SRX257686.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:57:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257686/SRX257686.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:57:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257686/SRX257686.05_summits.bed INFO @ Tue, 16 Jun 2020 08:57:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1127 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:57:40: 16000000 INFO @ Tue, 16 Jun 2020 08:57:43: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:57:43: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:57:43: #1 total tags in treatment: 16692815 INFO @ Tue, 16 Jun 2020 08:57:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:57:43: #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 08:57:44: #1 tags after filtering in treatment: 16692815 INFO @ Tue, 16 Jun 2020 08:57:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:57:44: #1 finished! INFO @ Tue, 16 Jun 2020 08:57:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:57:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:57:45: #2 number of paired peaks: 290 WARNING @ Tue, 16 Jun 2020 08:57:45: Fewer paired peaks (290) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 290 pairs to build model! INFO @ Tue, 16 Jun 2020 08:57:45: start model_add_line... INFO @ Tue, 16 Jun 2020 08:57:45: start X-correlation... INFO @ Tue, 16 Jun 2020 08:57:45: end of X-cor INFO @ Tue, 16 Jun 2020 08:57:45: #2 finished! INFO @ Tue, 16 Jun 2020 08:57:45: #2 predicted fragment length is 43 bps INFO @ Tue, 16 Jun 2020 08:57:45: #2 alternative fragment length(s) may be 1,43,571 bps INFO @ Tue, 16 Jun 2020 08:57:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257686/SRX257686.20_model.r WARNING @ Tue, 16 Jun 2020 08:57:45: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:57:45: #2 You may need to consider one of the other alternative d(s): 1,43,571 WARNING @ Tue, 16 Jun 2020 08:57:45: #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 08:57:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:57:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:57:55: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:58:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257686/SRX257686.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:58:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257686/SRX257686.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:58:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257686/SRX257686.10_summits.bed INFO @ Tue, 16 Jun 2020 08:58:10: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (468 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:58:13: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:58:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257686/SRX257686.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:58:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257686/SRX257686.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:58:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257686/SRX257686.20_summits.bed INFO @ Tue, 16 Jun 2020 08:58:27: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (158 records, 4 fields): 1 millis CompletedMACS2peakCalling