Job ID = 6366051 SRX = SRX059223 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:37:51 prefetch.2.10.7: 1) Downloading 'SRR190663'... 2020-06-15T22:37:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:39:59 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:40:00 prefetch.2.10.7: 'SRR190663' is valid 2020-06-15T22:40:00 prefetch.2.10.7: 1) 'SRR190663' was downloaded successfully Read 17396159 spots for SRR190663/SRR190663.sra Written 17396159 spots for SRR190663/SRR190663.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: 00:03:11 17396159 reads; of these: 17396159 (100.00%) were unpaired; of these: 266623 (1.53%) aligned 0 times 13791624 (79.28%) aligned exactly 1 time 3337912 (19.19%) aligned >1 times 98.47% overall alignment rate Time searching: 00:03:11 Overall time: 00:03:11 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] 2247750 / 17129536 = 0.1312 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 07:48:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059223/SRX059223.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059223/SRX059223.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059223/SRX059223.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059223/SRX059223.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 07:48:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:48:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:48:43: 1000000 INFO @ Tue, 16 Jun 2020 07:48:48: 2000000 INFO @ Tue, 16 Jun 2020 07:48:53: 3000000 INFO @ Tue, 16 Jun 2020 07:48:57: 4000000 INFO @ Tue, 16 Jun 2020 07:49:02: 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 07:49:07: 6000000 INFO @ Tue, 16 Jun 2020 07:49:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059223/SRX059223.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059223/SRX059223.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059223/SRX059223.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059223/SRX059223.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 07:49:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:49:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:49:12: 7000000 INFO @ Tue, 16 Jun 2020 07:49:13: 1000000 INFO @ Tue, 16 Jun 2020 07:49:17: 8000000 INFO @ Tue, 16 Jun 2020 07:49:18: 2000000 INFO @ Tue, 16 Jun 2020 07:49:22: 9000000 INFO @ Tue, 16 Jun 2020 07:49:23: 3000000 INFO @ Tue, 16 Jun 2020 07:49:27: 10000000 INFO @ Tue, 16 Jun 2020 07:49:28: 4000000 INFO @ Tue, 16 Jun 2020 07:49:32: 11000000 INFO @ Tue, 16 Jun 2020 07:49:33: 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 07:49:37: 12000000 INFO @ Tue, 16 Jun 2020 07:49:38: 6000000 INFO @ Tue, 16 Jun 2020 07:49:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059223/SRX059223.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059223/SRX059223.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059223/SRX059223.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059223/SRX059223.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 07:49:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:49:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:49:42: 13000000 INFO @ Tue, 16 Jun 2020 07:49:43: 7000000 INFO @ Tue, 16 Jun 2020 07:49:43: 1000000 INFO @ Tue, 16 Jun 2020 07:49:46: 14000000 INFO @ Tue, 16 Jun 2020 07:49:48: 8000000 INFO @ Tue, 16 Jun 2020 07:49:48: 2000000 INFO @ Tue, 16 Jun 2020 07:49:51: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 07:49:51: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 07:49:51: #1 total tags in treatment: 14881786 INFO @ Tue, 16 Jun 2020 07:49:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:49:51: #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 07:49:51: #1 tags after filtering in treatment: 14881786 INFO @ Tue, 16 Jun 2020 07:49:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:49:51: #1 finished! INFO @ Tue, 16 Jun 2020 07:49:51: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:49:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:49:52: #2 number of paired peaks: 254 WARNING @ Tue, 16 Jun 2020 07:49:52: Fewer paired peaks (254) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 254 pairs to build model! INFO @ Tue, 16 Jun 2020 07:49:52: start model_add_line... INFO @ Tue, 16 Jun 2020 07:49:52: start X-correlation... INFO @ Tue, 16 Jun 2020 07:49:52: end of X-cor INFO @ Tue, 16 Jun 2020 07:49:52: #2 finished! INFO @ Tue, 16 Jun 2020 07:49:52: #2 predicted fragment length is 40 bps INFO @ Tue, 16 Jun 2020 07:49:52: #2 alternative fragment length(s) may be 2,40,547 bps INFO @ Tue, 16 Jun 2020 07:49:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059223/SRX059223.05_model.r WARNING @ Tue, 16 Jun 2020 07:49:52: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:49:52: #2 You may need to consider one of the other alternative d(s): 2,40,547 WARNING @ Tue, 16 Jun 2020 07:49:52: #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 07:49:52: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:49:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:49:52: 9000000 INFO @ Tue, 16 Jun 2020 07:49:53: 3000000 INFO @ Tue, 16 Jun 2020 07:49:57: 10000000 INFO @ Tue, 16 Jun 2020 07:49:58: 4000000 INFO @ Tue, 16 Jun 2020 07:50:02: 11000000 INFO @ Tue, 16 Jun 2020 07:50:03: 5000000 INFO @ Tue, 16 Jun 2020 07:50:07: 12000000 INFO @ Tue, 16 Jun 2020 07:50:08: 6000000 INFO @ Tue, 16 Jun 2020 07:50:12: 13000000 INFO @ Tue, 16 Jun 2020 07:50:13: 7000000 INFO @ Tue, 16 Jun 2020 07:50:17: 14000000 INFO @ Tue, 16 Jun 2020 07:50:18: 8000000 INFO @ Tue, 16 Jun 2020 07:50:19: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:50:21: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 07:50:21: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 07:50:21: #1 total tags in treatment: 14881786 INFO @ Tue, 16 Jun 2020 07:50:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:50:21: #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 07:50:22: #1 tags after filtering in treatment: 14881786 INFO @ Tue, 16 Jun 2020 07:50:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:50:22: #1 finished! INFO @ Tue, 16 Jun 2020 07:50:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:50:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:50:23: #2 number of paired peaks: 254 WARNING @ Tue, 16 Jun 2020 07:50:23: Fewer paired peaks (254) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 254 pairs to build model! INFO @ Tue, 16 Jun 2020 07:50:23: start model_add_line... INFO @ Tue, 16 Jun 2020 07:50:23: 9000000 INFO @ Tue, 16 Jun 2020 07:50:23: start X-correlation... INFO @ Tue, 16 Jun 2020 07:50:23: end of X-cor INFO @ Tue, 16 Jun 2020 07:50:23: #2 finished! INFO @ Tue, 16 Jun 2020 07:50:23: #2 predicted fragment length is 40 bps INFO @ Tue, 16 Jun 2020 07:50:23: #2 alternative fragment length(s) may be 2,40,547 bps INFO @ Tue, 16 Jun 2020 07:50:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059223/SRX059223.10_model.r WARNING @ Tue, 16 Jun 2020 07:50:23: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:50:23: #2 You may need to consider one of the other alternative d(s): 2,40,547 WARNING @ Tue, 16 Jun 2020 07:50:23: #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 07:50:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:50:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:50:28: 10000000 INFO @ Tue, 16 Jun 2020 07:50:33: 11000000 INFO @ Tue, 16 Jun 2020 07:50:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059223/SRX059223.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:50:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059223/SRX059223.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:50:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059223/SRX059223.05_summits.bed INFO @ Tue, 16 Jun 2020 07:50:33: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (10858 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:50:38: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:50:42: 13000000 INFO @ Tue, 16 Jun 2020 07:50:47: 14000000 INFO @ Tue, 16 Jun 2020 07:50:50: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:50:52: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 07:50:52: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 07:50:52: #1 total tags in treatment: 14881786 INFO @ Tue, 16 Jun 2020 07:50:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:50:52: #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 07:50:52: #1 tags after filtering in treatment: 14881786 INFO @ Tue, 16 Jun 2020 07:50:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:50:52: #1 finished! INFO @ Tue, 16 Jun 2020 07:50:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:50:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:50:53: #2 number of paired peaks: 254 WARNING @ Tue, 16 Jun 2020 07:50:53: Fewer paired peaks (254) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 254 pairs to build model! INFO @ Tue, 16 Jun 2020 07:50:53: start model_add_line... INFO @ Tue, 16 Jun 2020 07:50:53: start X-correlation... INFO @ Tue, 16 Jun 2020 07:50:53: end of X-cor INFO @ Tue, 16 Jun 2020 07:50:53: #2 finished! INFO @ Tue, 16 Jun 2020 07:50:53: #2 predicted fragment length is 40 bps INFO @ Tue, 16 Jun 2020 07:50:53: #2 alternative fragment length(s) may be 2,40,547 bps INFO @ Tue, 16 Jun 2020 07:50:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059223/SRX059223.20_model.r WARNING @ Tue, 16 Jun 2020 07:50:53: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:50:53: #2 You may need to consider one of the other alternative d(s): 2,40,547 WARNING @ Tue, 16 Jun 2020 07:50:53: #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 07:50:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:50:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:51:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059223/SRX059223.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:51:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059223/SRX059223.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:51:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059223/SRX059223.10_summits.bed INFO @ Tue, 16 Jun 2020 07:51:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1619 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:51:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:51:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059223/SRX059223.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:51:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059223/SRX059223.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:51:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059223/SRX059223.20_summits.bed INFO @ Tue, 16 Jun 2020 07:51:39: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (162 records, 4 fields): 1 millis CompletedMACS2peakCalling