Job ID = 5790645 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 33,775,801 reads read : 67,551,602 reads written : 33,775,801 reads 0-length : 33,775,801 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:00:01 Multiseed full-index search: 03:23:02 33775801 reads; of these: 33775801 (100.00%) were unpaired; of these: 18455583 (54.64%) aligned 0 times 6518583 (19.30%) aligned exactly 1 time 8801635 (26.06%) aligned >1 times 45.36% overall alignment rate Time searching: 03:23:04 Overall time: 03:23:04 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 2510527 / 15320218 = 0.1639 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 @ Wed, 22 Apr 2020 08:37:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5299288/SRX5299288.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5299288/SRX5299288.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5299288/SRX5299288.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5299288/SRX5299288.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Wed, 22 Apr 2020 08:37:46: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:37:46: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:37:52: 1000000 INFO @ Wed, 22 Apr 2020 08:37:58: 2000000 INFO @ Wed, 22 Apr 2020 08:38:04: 3000000 INFO @ Wed, 22 Apr 2020 08:38:10: 4000000 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 @ Wed, 22 Apr 2020 08:38:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5299288/SRX5299288.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5299288/SRX5299288.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5299288/SRX5299288.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5299288/SRX5299288.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Wed, 22 Apr 2020 08:38:15: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:38:15: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:38:16: 5000000 INFO @ Wed, 22 Apr 2020 08:38:21: 1000000 INFO @ Wed, 22 Apr 2020 08:38:22: 6000000 INFO @ Wed, 22 Apr 2020 08:38:27: 2000000 INFO @ Wed, 22 Apr 2020 08:38:28: 7000000 INFO @ Wed, 22 Apr 2020 08:38:34: 3000000 INFO @ Wed, 22 Apr 2020 08:38:34: 8000000 INFO @ Wed, 22 Apr 2020 08:38:40: 4000000 INFO @ Wed, 22 Apr 2020 08:38:41: 9000000 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 @ Wed, 22 Apr 2020 08:38:46: 5000000 INFO @ Wed, 22 Apr 2020 08:38:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5299288/SRX5299288.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5299288/SRX5299288.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5299288/SRX5299288.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5299288/SRX5299288.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Wed, 22 Apr 2020 08:38:46: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:38:46: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:38:47: 10000000 INFO @ Wed, 22 Apr 2020 08:38:52: 6000000 INFO @ Wed, 22 Apr 2020 08:38:52: 1000000 INFO @ Wed, 22 Apr 2020 08:38:53: 11000000 INFO @ Wed, 22 Apr 2020 08:38:58: 7000000 INFO @ Wed, 22 Apr 2020 08:38:59: 2000000 INFO @ Wed, 22 Apr 2020 08:39:00: 12000000 INFO @ Wed, 22 Apr 2020 08:39:05: #1 tag size is determined as 102 bps INFO @ Wed, 22 Apr 2020 08:39:05: #1 tag size = 102 INFO @ Wed, 22 Apr 2020 08:39:05: #1 total tags in treatment: 12809691 INFO @ Wed, 22 Apr 2020 08:39:05: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:39:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 08:39:05: 8000000 INFO @ Wed, 22 Apr 2020 08:39:05: 3000000 INFO @ Wed, 22 Apr 2020 08:39:05: #1 tags after filtering in treatment: 12809520 INFO @ Wed, 22 Apr 2020 08:39:05: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 08:39:05: #1 finished! INFO @ Wed, 22 Apr 2020 08:39:05: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:39:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:39:08: #2 number of paired peaks: 103849 INFO @ Wed, 22 Apr 2020 08:39:08: start model_add_line... INFO @ Wed, 22 Apr 2020 08:39:09: start X-correlation... INFO @ Wed, 22 Apr 2020 08:39:09: end of X-cor INFO @ Wed, 22 Apr 2020 08:39:09: #2 finished! INFO @ Wed, 22 Apr 2020 08:39:09: #2 predicted fragment length is 109 bps INFO @ Wed, 22 Apr 2020 08:39:09: #2 alternative fragment length(s) may be 109 bps INFO @ Wed, 22 Apr 2020 08:39:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5299288/SRX5299288.05_model.r WARNING @ Wed, 22 Apr 2020 08:39:09: #2 Since the d (109) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:39:09: #2 You may need to consider one of the other alternative d(s): 109 WARNING @ Wed, 22 Apr 2020 08:39:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 08:39:09: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:39:09: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:39:11: 9000000 INFO @ Wed, 22 Apr 2020 08:39:11: 4000000 INFO @ Wed, 22 Apr 2020 08:39:17: 10000000 INFO @ Wed, 22 Apr 2020 08:39:17: 5000000 INFO @ Wed, 22 Apr 2020 08:39:23: 11000000 INFO @ Wed, 22 Apr 2020 08:39:24: 6000000 INFO @ Wed, 22 Apr 2020 08:39:30: 12000000 INFO @ Wed, 22 Apr 2020 08:39:30: 7000000 INFO @ Wed, 22 Apr 2020 08:39:35: #1 tag size is determined as 102 bps INFO @ Wed, 22 Apr 2020 08:39:35: #1 tag size = 102 INFO @ Wed, 22 Apr 2020 08:39:35: #1 total tags in treatment: 12809691 INFO @ Wed, 22 Apr 2020 08:39:35: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:39:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 08:39:35: #1 tags after filtering in treatment: 12809520 INFO @ Wed, 22 Apr 2020 08:39:35: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 08:39:35: #1 finished! INFO @ Wed, 22 Apr 2020 08:39:35: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:39:35: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:39:36: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:39:37: 8000000 INFO @ Wed, 22 Apr 2020 08:39:39: #2 number of paired peaks: 103849 INFO @ Wed, 22 Apr 2020 08:39:39: start model_add_line... INFO @ Wed, 22 Apr 2020 08:39:39: start X-correlation... INFO @ Wed, 22 Apr 2020 08:39:39: end of X-cor INFO @ Wed, 22 Apr 2020 08:39:39: #2 finished! INFO @ Wed, 22 Apr 2020 08:39:39: #2 predicted fragment length is 109 bps INFO @ Wed, 22 Apr 2020 08:39:39: #2 alternative fragment length(s) may be 109 bps INFO @ Wed, 22 Apr 2020 08:39:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5299288/SRX5299288.10_model.r WARNING @ Wed, 22 Apr 2020 08:39:39: #2 Since the d (109) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:39:39: #2 You may need to consider one of the other alternative d(s): 109 WARNING @ Wed, 22 Apr 2020 08:39:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 08:39:39: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:39:39: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:39:43: 9000000 INFO @ Wed, 22 Apr 2020 08:39:49: 10000000 INFO @ Wed, 22 Apr 2020 08:39:52: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5299288/SRX5299288.05_peaks.xls INFO @ Wed, 22 Apr 2020 08:39:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5299288/SRX5299288.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:39:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5299288/SRX5299288.05_summits.bed INFO @ Wed, 22 Apr 2020 08:39:52: Done! INFO @ Wed, 22 Apr 2020 08:39:55: 11000000 pass1 - making usageList (166 chroms): 6 millis pass2 - checking and writing primary data (44117 records, 4 fields): 41 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:40:01: 12000000 INFO @ Wed, 22 Apr 2020 08:40:06: #1 tag size is determined as 102 bps INFO @ Wed, 22 Apr 2020 08:40:06: #1 tag size = 102 INFO @ Wed, 22 Apr 2020 08:40:06: #1 total tags in treatment: 12809691 INFO @ Wed, 22 Apr 2020 08:40:06: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:40:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 08:40:06: #1 tags after filtering in treatment: 12809520 INFO @ Wed, 22 Apr 2020 08:40:06: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 08:40:06: #1 finished! INFO @ Wed, 22 Apr 2020 08:40:06: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:40:06: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:40:08: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:40:10: #2 number of paired peaks: 103849 INFO @ Wed, 22 Apr 2020 08:40:10: start model_add_line... INFO @ Wed, 22 Apr 2020 08:40:10: start X-correlation... INFO @ Wed, 22 Apr 2020 08:40:10: end of X-cor INFO @ Wed, 22 Apr 2020 08:40:10: #2 finished! INFO @ Wed, 22 Apr 2020 08:40:10: #2 predicted fragment length is 109 bps INFO @ Wed, 22 Apr 2020 08:40:10: #2 alternative fragment length(s) may be 109 bps INFO @ Wed, 22 Apr 2020 08:40:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5299288/SRX5299288.20_model.r WARNING @ Wed, 22 Apr 2020 08:40:10: #2 Since the d (109) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:40:10: #2 You may need to consider one of the other alternative d(s): 109 WARNING @ Wed, 22 Apr 2020 08:40:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 08:40:10: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:40:10: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:40:23: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5299288/SRX5299288.10_peaks.xls INFO @ Wed, 22 Apr 2020 08:40:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5299288/SRX5299288.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:40:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5299288/SRX5299288.10_summits.bed INFO @ Wed, 22 Apr 2020 08:40:23: Done! pass1 - making usageList (95 chroms): 2 millis pass2 - checking and writing primary data (11089 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:40:39: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:40:55: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5299288/SRX5299288.20_peaks.xls INFO @ Wed, 22 Apr 2020 08:40:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5299288/SRX5299288.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:40:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5299288/SRX5299288.20_summits.bed INFO @ Wed, 22 Apr 2020 08:40:55: Done! pass1 - making usageList (49 chroms): 1 millis pass2 - checking and writing primary data (1364 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。