Job ID = 6497537 SRX = SRX514569 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:16:29 prefetch.2.10.7: 1) Downloading 'SRR1230857'... 2020-06-25T22:16:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:18:58 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:18:58 prefetch.2.10.7: 1) 'SRR1230857' was downloaded successfully Read 22858982 spots for SRR1230857/SRR1230857.sra Written 22858982 spots for SRR1230857/SRR1230857.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: 00:05:10 22858982 reads; of these: 22858982 (100.00%) were unpaired; of these: 654843 (2.86%) aligned 0 times 18698113 (81.80%) aligned exactly 1 time 3506026 (15.34%) aligned >1 times 97.14% overall alignment rate Time searching: 00:05:10 Overall time: 00:05:10 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] 8947778 / 22204139 = 0.4030 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 @ Fri, 26 Jun 2020 07:31:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX514569/SRX514569.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX514569/SRX514569.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX514569/SRX514569.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX514569/SRX514569.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 @ Fri, 26 Jun 2020 07:31:43: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:31:43: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:31:49: 1000000 INFO @ Fri, 26 Jun 2020 07:31:54: 2000000 INFO @ Fri, 26 Jun 2020 07:32:00: 3000000 INFO @ Fri, 26 Jun 2020 07:32:05: 4000000 INFO @ Fri, 26 Jun 2020 07:32:10: 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 @ Fri, 26 Jun 2020 07:32:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX514569/SRX514569.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX514569/SRX514569.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX514569/SRX514569.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX514569/SRX514569.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 @ Fri, 26 Jun 2020 07:32:13: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:32:13: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:32:16: 6000000 INFO @ Fri, 26 Jun 2020 07:32:19: 1000000 INFO @ Fri, 26 Jun 2020 07:32:22: 7000000 INFO @ Fri, 26 Jun 2020 07:32:24: 2000000 INFO @ Fri, 26 Jun 2020 07:32:28: 8000000 INFO @ Fri, 26 Jun 2020 07:32:30: 3000000 INFO @ Fri, 26 Jun 2020 07:32:34: 9000000 INFO @ Fri, 26 Jun 2020 07:32:36: 4000000 INFO @ Fri, 26 Jun 2020 07:32:40: 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 @ Fri, 26 Jun 2020 07:32:42: 5000000 INFO @ Fri, 26 Jun 2020 07:32:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX514569/SRX514569.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX514569/SRX514569.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX514569/SRX514569.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX514569/SRX514569.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 @ Fri, 26 Jun 2020 07:32:43: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:32:43: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:32:46: 11000000 INFO @ Fri, 26 Jun 2020 07:32:48: 6000000 INFO @ Fri, 26 Jun 2020 07:32:50: 1000000 INFO @ Fri, 26 Jun 2020 07:32:52: 12000000 INFO @ Fri, 26 Jun 2020 07:32:54: 7000000 INFO @ Fri, 26 Jun 2020 07:32:56: 2000000 INFO @ Fri, 26 Jun 2020 07:32:58: 13000000 INFO @ Fri, 26 Jun 2020 07:32:59: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:32:59: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:32:59: #1 total tags in treatment: 13256361 INFO @ Fri, 26 Jun 2020 07:32:59: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:32:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:33:00: #1 tags after filtering in treatment: 13256361 INFO @ Fri, 26 Jun 2020 07:33:00: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:33:00: #1 finished! INFO @ Fri, 26 Jun 2020 07:33:00: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:33:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:33:00: 8000000 INFO @ Fri, 26 Jun 2020 07:33:01: #2 number of paired peaks: 327 WARNING @ Fri, 26 Jun 2020 07:33:01: Fewer paired peaks (327) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 327 pairs to build model! INFO @ Fri, 26 Jun 2020 07:33:01: start model_add_line... INFO @ Fri, 26 Jun 2020 07:33:01: start X-correlation... INFO @ Fri, 26 Jun 2020 07:33:01: end of X-cor INFO @ Fri, 26 Jun 2020 07:33:01: #2 finished! INFO @ Fri, 26 Jun 2020 07:33:01: #2 predicted fragment length is 50 bps INFO @ Fri, 26 Jun 2020 07:33:01: #2 alternative fragment length(s) may be 2,50,574 bps INFO @ Fri, 26 Jun 2020 07:33:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX514569/SRX514569.05_model.r WARNING @ Fri, 26 Jun 2020 07:33:01: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:33:01: #2 You may need to consider one of the other alternative d(s): 2,50,574 WARNING @ Fri, 26 Jun 2020 07:33:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:33:01: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:33:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:33:03: 3000000 INFO @ Fri, 26 Jun 2020 07:33:05: 9000000 INFO @ Fri, 26 Jun 2020 07:33:10: 4000000 INFO @ Fri, 26 Jun 2020 07:33:11: 10000000 INFO @ Fri, 26 Jun 2020 07:33:16: 5000000 INFO @ Fri, 26 Jun 2020 07:33:17: 11000000 INFO @ Fri, 26 Jun 2020 07:33:22: 12000000 INFO @ Fri, 26 Jun 2020 07:33:23: 6000000 INFO @ Fri, 26 Jun 2020 07:33:23: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:33:27: 13000000 INFO @ Fri, 26 Jun 2020 07:33:29: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:33:29: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:33:29: #1 total tags in treatment: 13256361 INFO @ Fri, 26 Jun 2020 07:33:29: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:33:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:33:29: #1 tags after filtering in treatment: 13256361 INFO @ Fri, 26 Jun 2020 07:33:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:33:29: #1 finished! INFO @ Fri, 26 Jun 2020 07:33:29: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:33:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:33:30: 7000000 INFO @ Fri, 26 Jun 2020 07:33:30: #2 number of paired peaks: 327 WARNING @ Fri, 26 Jun 2020 07:33:30: Fewer paired peaks (327) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 327 pairs to build model! INFO @ Fri, 26 Jun 2020 07:33:30: start model_add_line... INFO @ Fri, 26 Jun 2020 07:33:30: start X-correlation... INFO @ Fri, 26 Jun 2020 07:33:30: end of X-cor INFO @ Fri, 26 Jun 2020 07:33:30: #2 finished! INFO @ Fri, 26 Jun 2020 07:33:30: #2 predicted fragment length is 50 bps INFO @ Fri, 26 Jun 2020 07:33:30: #2 alternative fragment length(s) may be 2,50,574 bps INFO @ Fri, 26 Jun 2020 07:33:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX514569/SRX514569.10_model.r WARNING @ Fri, 26 Jun 2020 07:33:30: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:33:30: #2 You may need to consider one of the other alternative d(s): 2,50,574 WARNING @ Fri, 26 Jun 2020 07:33:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:33:30: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:33:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:33:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX514569/SRX514569.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:33:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX514569/SRX514569.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:33:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX514569/SRX514569.05_summits.bed INFO @ Fri, 26 Jun 2020 07:33:34: Done! INFO @ Fri, 26 Jun 2020 07:33:36: 8000000 pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (749 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:33:42: 9000000 INFO @ Fri, 26 Jun 2020 07:33:47: 10000000 INFO @ Fri, 26 Jun 2020 07:33:53: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:33:53: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:33:59: 12000000 INFO @ Fri, 26 Jun 2020 07:34:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX514569/SRX514569.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:34:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX514569/SRX514569.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:34:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX514569/SRX514569.10_summits.bed INFO @ Fri, 26 Jun 2020 07:34:03: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (474 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:34:05: 13000000 INFO @ Fri, 26 Jun 2020 07:34:07: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:34:07: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:34:07: #1 total tags in treatment: 13256361 INFO @ Fri, 26 Jun 2020 07:34:07: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:34:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:34:07: #1 tags after filtering in treatment: 13256361 INFO @ Fri, 26 Jun 2020 07:34:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:34:07: #1 finished! INFO @ Fri, 26 Jun 2020 07:34:07: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:34:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:34:08: #2 number of paired peaks: 327 WARNING @ Fri, 26 Jun 2020 07:34:08: Fewer paired peaks (327) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 327 pairs to build model! INFO @ Fri, 26 Jun 2020 07:34:08: start model_add_line... INFO @ Fri, 26 Jun 2020 07:34:08: start X-correlation... INFO @ Fri, 26 Jun 2020 07:34:08: end of X-cor INFO @ Fri, 26 Jun 2020 07:34:08: #2 finished! INFO @ Fri, 26 Jun 2020 07:34:08: #2 predicted fragment length is 50 bps INFO @ Fri, 26 Jun 2020 07:34:08: #2 alternative fragment length(s) may be 2,50,574 bps INFO @ Fri, 26 Jun 2020 07:34:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX514569/SRX514569.20_model.r WARNING @ Fri, 26 Jun 2020 07:34:08: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:34:08: #2 You may need to consider one of the other alternative d(s): 2,50,574 WARNING @ Fri, 26 Jun 2020 07:34:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:34:08: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:34:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:34:31: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:34:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX514569/SRX514569.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:34:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX514569/SRX514569.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:34:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX514569/SRX514569.20_summits.bed INFO @ Fri, 26 Jun 2020 07:34:42: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (173 records, 4 fields): 2 millis CompletedMACS2peakCalling