Job ID = 5790776 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 15,172,892 reads read : 30,345,784 reads written : 15,172,892 reads 0-length : 15,172,892 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: 00:09:24 15172892 reads; of these: 15172892 (100.00%) were unpaired; of these: 5478360 (36.11%) aligned 0 times 7167347 (47.24%) aligned exactly 1 time 2527185 (16.66%) aligned >1 times 63.89% overall alignment rate Time searching: 00:09:27 Overall time: 00:09:27 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_rmdupse_core] 738044 / 9694532 = 0.0761 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 07:12:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX7625150/SRX7625150.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX7625150/SRX7625150.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX7625150/SRX7625150.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX7625150/SRX7625150.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 07:12:38: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:12:38: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:12:44: 1000000 INFO @ Wed, 22 Apr 2020 07:12:49: 2000000 INFO @ Wed, 22 Apr 2020 07:12:55: 3000000 INFO @ Wed, 22 Apr 2020 07:13:01: 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 07:13:07: 5000000 INFO @ Wed, 22 Apr 2020 07:13:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX7625150/SRX7625150.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX7625150/SRX7625150.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX7625150/SRX7625150.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX7625150/SRX7625150.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 07:13:08: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:13:08: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:13:13: 6000000 INFO @ Wed, 22 Apr 2020 07:13:14: 1000000 INFO @ Wed, 22 Apr 2020 07:13:19: 7000000 INFO @ Wed, 22 Apr 2020 07:13:20: 2000000 INFO @ Wed, 22 Apr 2020 07:13:25: 8000000 INFO @ Wed, 22 Apr 2020 07:13:27: 3000000 INFO @ Wed, 22 Apr 2020 07:13:31: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 07:13:31: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 07:13:31: #1 total tags in treatment: 8956488 INFO @ Wed, 22 Apr 2020 07:13:31: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:13:31: #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 07:13:32: #1 tags after filtering in treatment: 8956251 INFO @ Wed, 22 Apr 2020 07:13:32: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:13:32: #1 finished! INFO @ Wed, 22 Apr 2020 07:13:32: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:13:32: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:13:33: #2 number of paired peaks: 5328 INFO @ Wed, 22 Apr 2020 07:13:33: start model_add_line... INFO @ Wed, 22 Apr 2020 07:13:33: start X-correlation... INFO @ Wed, 22 Apr 2020 07:13:33: end of X-cor INFO @ Wed, 22 Apr 2020 07:13:33: #2 finished! INFO @ Wed, 22 Apr 2020 07:13:33: #2 predicted fragment length is 74 bps INFO @ Wed, 22 Apr 2020 07:13:33: #2 alternative fragment length(s) may be 74,518 bps INFO @ Wed, 22 Apr 2020 07:13:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX7625150/SRX7625150.05_model.r WARNING @ Wed, 22 Apr 2020 07:13:33: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:13:33: #2 You may need to consider one of the other alternative d(s): 74,518 WARNING @ Wed, 22 Apr 2020 07:13:33: #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 07:13:33: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:13:33: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:13:33: 4000000 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 07:13:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX7625150/SRX7625150.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX7625150/SRX7625150.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX7625150/SRX7625150.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX7625150/SRX7625150.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 07:13:37: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:13:37: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:13:39: 5000000 INFO @ Wed, 22 Apr 2020 07:13:44: 1000000 INFO @ Wed, 22 Apr 2020 07:13:45: 6000000 INFO @ Wed, 22 Apr 2020 07:13:50: 2000000 INFO @ Wed, 22 Apr 2020 07:13:52: 7000000 INFO @ Wed, 22 Apr 2020 07:13:52: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:13:56: 3000000 INFO @ Wed, 22 Apr 2020 07:13:58: 8000000 INFO @ Wed, 22 Apr 2020 07:14:02: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX7625150/SRX7625150.05_peaks.xls INFO @ Wed, 22 Apr 2020 07:14:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX7625150/SRX7625150.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:14:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX7625150/SRX7625150.05_summits.bed INFO @ Wed, 22 Apr 2020 07:14:02: Done! INFO @ Wed, 22 Apr 2020 07:14:03: 4000000 INFO @ Wed, 22 Apr 2020 07:14:04: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 07:14:04: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 07:14:04: #1 total tags in treatment: 8956488 INFO @ Wed, 22 Apr 2020 07:14:04: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:14:04: #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 07:14:04: #1 tags after filtering in treatment: 8956251 INFO @ Wed, 22 Apr 2020 07:14:04: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:14:04: #1 finished! INFO @ Wed, 22 Apr 2020 07:14:04: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:14:04: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:14:06: #2 number of paired peaks: 5328 INFO @ Wed, 22 Apr 2020 07:14:06: start model_add_line... INFO @ Wed, 22 Apr 2020 07:14:06: start X-correlation... INFO @ Wed, 22 Apr 2020 07:14:06: end of X-cor INFO @ Wed, 22 Apr 2020 07:14:06: #2 finished! INFO @ Wed, 22 Apr 2020 07:14:06: #2 predicted fragment length is 74 bps INFO @ Wed, 22 Apr 2020 07:14:06: #2 alternative fragment length(s) may be 74,518 bps INFO @ Wed, 22 Apr 2020 07:14:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX7625150/SRX7625150.10_model.r WARNING @ Wed, 22 Apr 2020 07:14:06: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:14:06: #2 You may need to consider one of the other alternative d(s): 74,518 WARNING @ Wed, 22 Apr 2020 07:14:06: #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 07:14:06: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:14:06: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (57 chroms): 1 millis pass2 - checking and writing primary data (765 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 07:14:09: 5000000 INFO @ Wed, 22 Apr 2020 07:14:15: 6000000 INFO @ Wed, 22 Apr 2020 07:14:20: 7000000 INFO @ Wed, 22 Apr 2020 07:14:25: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:14:26: 8000000 INFO @ Wed, 22 Apr 2020 07:14:32: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 07:14:32: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 07:14:32: #1 total tags in treatment: 8956488 INFO @ Wed, 22 Apr 2020 07:14:32: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:14:32: #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 07:14:32: #1 tags after filtering in treatment: 8956251 INFO @ Wed, 22 Apr 2020 07:14:32: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:14:32: #1 finished! INFO @ Wed, 22 Apr 2020 07:14:32: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:14:32: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:14:33: #2 number of paired peaks: 5328 INFO @ Wed, 22 Apr 2020 07:14:33: start model_add_line... INFO @ Wed, 22 Apr 2020 07:14:33: start X-correlation... INFO @ Wed, 22 Apr 2020 07:14:33: end of X-cor INFO @ Wed, 22 Apr 2020 07:14:33: #2 finished! INFO @ Wed, 22 Apr 2020 07:14:33: #2 predicted fragment length is 74 bps INFO @ Wed, 22 Apr 2020 07:14:33: #2 alternative fragment length(s) may be 74,518 bps INFO @ Wed, 22 Apr 2020 07:14:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX7625150/SRX7625150.20_model.r WARNING @ Wed, 22 Apr 2020 07:14:33: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:14:33: #2 You may need to consider one of the other alternative d(s): 74,518 WARNING @ Wed, 22 Apr 2020 07:14:33: #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 07:14:33: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:14:33: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:14:35: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX7625150/SRX7625150.10_peaks.xls INFO @ Wed, 22 Apr 2020 07:14:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX7625150/SRX7625150.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:14:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX7625150/SRX7625150.10_summits.bed INFO @ Wed, 22 Apr 2020 07:14:35: Done! pass1 - making usageList (54 chroms): 0 millis pass2 - checking and writing primary data (472 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 07:14:52: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:15:03: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX7625150/SRX7625150.20_peaks.xls INFO @ Wed, 22 Apr 2020 07:15:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX7625150/SRX7625150.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:15:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX7625150/SRX7625150.20_summits.bed INFO @ Wed, 22 Apr 2020 07:15:03: Done! pass1 - making usageList (44 chroms): 1 millis pass2 - checking and writing primary data (260 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。