Job ID = 5790637 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 35,166,479 reads read : 70,332,958 reads written : 35,166,479 reads 0-length : 35,166,479 spots read : 25,492,055 reads read : 50,984,110 reads written : 25,492,055 reads 0-length : 25,492,055 fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:43:31 60658534 reads; of these: 60658534 (100.00%) were unpaired; of these: 9775057 (16.11%) aligned 0 times 46326160 (76.37%) aligned exactly 1 time 4557317 (7.51%) aligned >1 times 83.89% overall alignment rate Time searching: 00:43:34 Overall time: 00:43:34 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 24 files... [bam_rmdupse_core] 27092857 / 50883477 = 0.5324 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 06:10:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5299281/SRX5299281.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5299281/SRX5299281.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5299281/SRX5299281.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5299281/SRX5299281.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 06:10:09: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:10:09: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:10:16: 1000000 INFO @ Wed, 22 Apr 2020 06:10:23: 2000000 INFO @ Wed, 22 Apr 2020 06:10:30: 3000000 INFO @ Wed, 22 Apr 2020 06:10:36: 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 06:10:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5299281/SRX5299281.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5299281/SRX5299281.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5299281/SRX5299281.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5299281/SRX5299281.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 06:10:39: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:10:39: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:10:43: 5000000 INFO @ Wed, 22 Apr 2020 06:10:47: 1000000 INFO @ Wed, 22 Apr 2020 06:10:50: 6000000 INFO @ Wed, 22 Apr 2020 06:10:56: 2000000 INFO @ Wed, 22 Apr 2020 06:10:56: 7000000 INFO @ Wed, 22 Apr 2020 06:11:03: 8000000 INFO @ Wed, 22 Apr 2020 06:11:04: 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 @ Wed, 22 Apr 2020 06:11:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5299281/SRX5299281.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5299281/SRX5299281.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5299281/SRX5299281.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5299281/SRX5299281.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 06:11:09: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:11:09: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:11:10: 9000000 INFO @ Wed, 22 Apr 2020 06:11:12: 4000000 INFO @ Wed, 22 Apr 2020 06:11:17: 10000000 INFO @ Wed, 22 Apr 2020 06:11:17: 1000000 INFO @ Wed, 22 Apr 2020 06:11:21: 5000000 INFO @ Wed, 22 Apr 2020 06:11:23: 11000000 INFO @ Wed, 22 Apr 2020 06:11:24: 2000000 INFO @ Wed, 22 Apr 2020 06:11:29: 6000000 INFO @ Wed, 22 Apr 2020 06:11:30: 12000000 INFO @ Wed, 22 Apr 2020 06:11:31: 3000000 INFO @ Wed, 22 Apr 2020 06:11:37: 7000000 INFO @ Wed, 22 Apr 2020 06:11:37: 13000000 INFO @ Wed, 22 Apr 2020 06:11:37: 4000000 INFO @ Wed, 22 Apr 2020 06:11:44: 8000000 INFO @ Wed, 22 Apr 2020 06:11:44: 14000000 INFO @ Wed, 22 Apr 2020 06:11:44: 5000000 INFO @ Wed, 22 Apr 2020 06:11:51: 9000000 INFO @ Wed, 22 Apr 2020 06:11:51: 6000000 INFO @ Wed, 22 Apr 2020 06:11:51: 15000000 INFO @ Wed, 22 Apr 2020 06:11:58: 16000000 INFO @ Wed, 22 Apr 2020 06:11:58: 7000000 INFO @ Wed, 22 Apr 2020 06:11:59: 10000000 INFO @ Wed, 22 Apr 2020 06:12:04: 17000000 INFO @ Wed, 22 Apr 2020 06:12:05: 8000000 INFO @ Wed, 22 Apr 2020 06:12:06: 11000000 INFO @ Wed, 22 Apr 2020 06:12:11: 18000000 INFO @ Wed, 22 Apr 2020 06:12:12: 9000000 INFO @ Wed, 22 Apr 2020 06:12:13: 12000000 INFO @ Wed, 22 Apr 2020 06:12:18: 19000000 INFO @ Wed, 22 Apr 2020 06:12:18: 10000000 INFO @ Wed, 22 Apr 2020 06:12:19: 13000000 INFO @ Wed, 22 Apr 2020 06:12:25: 14000000 INFO @ Wed, 22 Apr 2020 06:12:25: 20000000 INFO @ Wed, 22 Apr 2020 06:12:25: 11000000 INFO @ Wed, 22 Apr 2020 06:12:31: 15000000 INFO @ Wed, 22 Apr 2020 06:12:32: 12000000 INFO @ Wed, 22 Apr 2020 06:12:33: 21000000 INFO @ Wed, 22 Apr 2020 06:12:37: 16000000 INFO @ Wed, 22 Apr 2020 06:12:38: 13000000 INFO @ Wed, 22 Apr 2020 06:12:39: 22000000 INFO @ Wed, 22 Apr 2020 06:12:43: 17000000 INFO @ Wed, 22 Apr 2020 06:12:45: 14000000 INFO @ Wed, 22 Apr 2020 06:12:46: 23000000 INFO @ Wed, 22 Apr 2020 06:12:49: 18000000 INFO @ Wed, 22 Apr 2020 06:12:51: #1 tag size is determined as 102 bps INFO @ Wed, 22 Apr 2020 06:12:51: #1 tag size = 102 INFO @ Wed, 22 Apr 2020 06:12:51: #1 total tags in treatment: 23790620 INFO @ Wed, 22 Apr 2020 06:12:51: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:12:51: #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 06:12:51: 15000000 INFO @ Wed, 22 Apr 2020 06:12:52: #1 tags after filtering in treatment: 23790390 INFO @ Wed, 22 Apr 2020 06:12:52: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:12:52: #1 finished! INFO @ Wed, 22 Apr 2020 06:12:52: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:12:52: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:12:54: #2 number of paired peaks: 22372 INFO @ Wed, 22 Apr 2020 06:12:54: start model_add_line... INFO @ Wed, 22 Apr 2020 06:12:55: start X-correlation... INFO @ Wed, 22 Apr 2020 06:12:55: end of X-cor INFO @ Wed, 22 Apr 2020 06:12:55: #2 finished! INFO @ Wed, 22 Apr 2020 06:12:55: #2 predicted fragment length is 172 bps INFO @ Wed, 22 Apr 2020 06:12:55: #2 alternative fragment length(s) may be 172 bps INFO @ Wed, 22 Apr 2020 06:12:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5299281/SRX5299281.05_model.r WARNING @ Wed, 22 Apr 2020 06:12:55: #2 Since the d (172) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 06:12:55: #2 You may need to consider one of the other alternative d(s): 172 WARNING @ Wed, 22 Apr 2020 06:12:55: #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 06:12:55: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:12:55: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:12:56: 19000000 INFO @ Wed, 22 Apr 2020 06:12:58: 16000000 INFO @ Wed, 22 Apr 2020 06:13:04: 17000000 INFO @ Wed, 22 Apr 2020 06:13:04: 20000000 INFO @ Wed, 22 Apr 2020 06:13:11: 18000000 INFO @ Wed, 22 Apr 2020 06:13:12: 21000000 INFO @ Wed, 22 Apr 2020 06:13:17: 19000000 INFO @ Wed, 22 Apr 2020 06:13:20: 22000000 INFO @ Wed, 22 Apr 2020 06:13:23: 20000000 INFO @ Wed, 22 Apr 2020 06:13:28: 23000000 INFO @ Wed, 22 Apr 2020 06:13:30: 21000000 INFO @ Wed, 22 Apr 2020 06:13:34: #1 tag size is determined as 102 bps INFO @ Wed, 22 Apr 2020 06:13:34: #1 tag size = 102 INFO @ Wed, 22 Apr 2020 06:13:34: #1 total tags in treatment: 23790620 INFO @ Wed, 22 Apr 2020 06:13:34: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:13:34: #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 06:13:35: #1 tags after filtering in treatment: 23790390 INFO @ Wed, 22 Apr 2020 06:13:35: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:13:35: #1 finished! INFO @ Wed, 22 Apr 2020 06:13:35: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:13:35: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:13:36: 22000000 INFO @ Wed, 22 Apr 2020 06:13:37: #2 number of paired peaks: 22372 INFO @ Wed, 22 Apr 2020 06:13:37: start model_add_line... INFO @ Wed, 22 Apr 2020 06:13:37: start X-correlation... INFO @ Wed, 22 Apr 2020 06:13:37: end of X-cor INFO @ Wed, 22 Apr 2020 06:13:37: #2 finished! INFO @ Wed, 22 Apr 2020 06:13:37: #2 predicted fragment length is 172 bps INFO @ Wed, 22 Apr 2020 06:13:37: #2 alternative fragment length(s) may be 172 bps INFO @ Wed, 22 Apr 2020 06:13:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5299281/SRX5299281.10_model.r WARNING @ Wed, 22 Apr 2020 06:13:37: #2 Since the d (172) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 06:13:37: #2 You may need to consider one of the other alternative d(s): 172 WARNING @ Wed, 22 Apr 2020 06:13:37: #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 06:13:37: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:13:37: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:13:43: 23000000 INFO @ Wed, 22 Apr 2020 06:13:46: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:13:48: #1 tag size is determined as 102 bps INFO @ Wed, 22 Apr 2020 06:13:48: #1 tag size = 102 INFO @ Wed, 22 Apr 2020 06:13:48: #1 total tags in treatment: 23790620 INFO @ Wed, 22 Apr 2020 06:13:48: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:13:48: #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 06:13:48: #1 tags after filtering in treatment: 23790390 INFO @ Wed, 22 Apr 2020 06:13:48: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:13:48: #1 finished! INFO @ Wed, 22 Apr 2020 06:13:48: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:13:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:13:51: #2 number of paired peaks: 22372 INFO @ Wed, 22 Apr 2020 06:13:51: start model_add_line... INFO @ Wed, 22 Apr 2020 06:13:51: start X-correlation... INFO @ Wed, 22 Apr 2020 06:13:51: end of X-cor INFO @ Wed, 22 Apr 2020 06:13:51: #2 finished! INFO @ Wed, 22 Apr 2020 06:13:51: #2 predicted fragment length is 172 bps INFO @ Wed, 22 Apr 2020 06:13:51: #2 alternative fragment length(s) may be 172 bps INFO @ Wed, 22 Apr 2020 06:13:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5299281/SRX5299281.20_model.r WARNING @ Wed, 22 Apr 2020 06:13:51: #2 Since the d (172) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 06:13:51: #2 You may need to consider one of the other alternative d(s): 172 WARNING @ Wed, 22 Apr 2020 06:13:51: #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 06:13:51: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:13:51: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:14:13: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5299281/SRX5299281.05_peaks.xls INFO @ Wed, 22 Apr 2020 06:14:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5299281/SRX5299281.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:14:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5299281/SRX5299281.05_summits.bed INFO @ Wed, 22 Apr 2020 06:14:13: Done! pass1 - making usageList (135 chroms): 4 millis pass2 - checking and writing primary data (25721 records, 4 fields): 26 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 06:14:37: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:14:41: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 06:15:07: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5299281/SRX5299281.10_peaks.xls INFO @ Wed, 22 Apr 2020 06:15:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5299281/SRX5299281.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:15:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5299281/SRX5299281.10_summits.bed INFO @ Wed, 22 Apr 2020 06:15:07: Done! pass1 - making usageList (121 chroms): 3 millis pass2 - checking and writing primary data (22710 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:15:08: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5299281/SRX5299281.20_peaks.xls INFO @ Wed, 22 Apr 2020 06:15:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5299281/SRX5299281.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:15:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5299281/SRX5299281.20_summits.bed INFO @ Wed, 22 Apr 2020 06:15:08: Done! pass1 - making usageList (110 chroms): 3 millis pass2 - checking and writing primary data (20262 records, 4 fields): 21 millis CompletedMACS2peakCalling