Job ID = 5790805 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,036,633 reads read : 34,073,266 reads written : 17,036,633 reads 0-length : 17,036,633 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: 00:00:00 Multiseed full-index search: 00:10:14 17036633 reads; of these: 17036633 (100.00%) were unpaired; of these: 1255592 (7.37%) aligned 0 times 11080251 (65.04%) aligned exactly 1 time 4700790 (27.59%) aligned >1 times 92.63% overall alignment rate Time searching: 00:10:15 Overall time: 00:10:15 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] 4466953 / 15781041 = 0.2831 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 07:48:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX7625167/SRX7625167.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX7625167/SRX7625167.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX7625167/SRX7625167.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX7625167/SRX7625167.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 07:48:48: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:48:48: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:48:55: 1000000 INFO @ Wed, 22 Apr 2020 07:49:03: 2000000 INFO @ Wed, 22 Apr 2020 07:49:11: 3000000 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 07:49:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX7625167/SRX7625167.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX7625167/SRX7625167.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX7625167/SRX7625167.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX7625167/SRX7625167.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 07:49:18: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:49:18: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:49:18: 4000000 INFO @ Wed, 22 Apr 2020 07:49:26: 1000000 INFO @ Wed, 22 Apr 2020 07:49:27: 5000000 INFO @ Wed, 22 Apr 2020 07:49:35: 2000000 INFO @ Wed, 22 Apr 2020 07:49:35: 6000000 INFO @ Wed, 22 Apr 2020 07:49:44: 7000000 INFO @ Wed, 22 Apr 2020 07:49:44: 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 07:49:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX7625167/SRX7625167.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX7625167/SRX7625167.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX7625167/SRX7625167.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX7625167/SRX7625167.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 07:49:48: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:49:48: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:49:52: 8000000 INFO @ Wed, 22 Apr 2020 07:49:52: 4000000 INFO @ Wed, 22 Apr 2020 07:49:56: 1000000 INFO @ Wed, 22 Apr 2020 07:50:00: 9000000 INFO @ Wed, 22 Apr 2020 07:50:01: 5000000 INFO @ Wed, 22 Apr 2020 07:50:05: 2000000 INFO @ Wed, 22 Apr 2020 07:50:09: 10000000 INFO @ Wed, 22 Apr 2020 07:50:10: 6000000 INFO @ Wed, 22 Apr 2020 07:50:14: 3000000 INFO @ Wed, 22 Apr 2020 07:50:17: 11000000 INFO @ Wed, 22 Apr 2020 07:50:18: 7000000 INFO @ Wed, 22 Apr 2020 07:50:20: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 07:50:20: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 07:50:20: #1 total tags in treatment: 11314088 INFO @ Wed, 22 Apr 2020 07:50:20: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:50:20: #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 07:50:20: #1 tags after filtering in treatment: 11313891 INFO @ Wed, 22 Apr 2020 07:50:20: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:50:20: #1 finished! INFO @ Wed, 22 Apr 2020 07:50:20: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:50:20: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:50:21: #2 number of paired peaks: 5056 INFO @ Wed, 22 Apr 2020 07:50:21: start model_add_line... INFO @ Wed, 22 Apr 2020 07:50:22: start X-correlation... INFO @ Wed, 22 Apr 2020 07:50:22: end of X-cor INFO @ Wed, 22 Apr 2020 07:50:22: #2 finished! INFO @ Wed, 22 Apr 2020 07:50:22: #2 predicted fragment length is 73 bps INFO @ Wed, 22 Apr 2020 07:50:22: #2 alternative fragment length(s) may be 73 bps INFO @ Wed, 22 Apr 2020 07:50:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX7625167/SRX7625167.05_model.r WARNING @ Wed, 22 Apr 2020 07:50:22: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:50:22: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Wed, 22 Apr 2020 07:50:22: #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 07:50:22: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:50:22: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:50:22: 4000000 INFO @ Wed, 22 Apr 2020 07:50:26: 8000000 INFO @ Wed, 22 Apr 2020 07:50:30: 5000000 INFO @ Wed, 22 Apr 2020 07:50:35: 9000000 INFO @ Wed, 22 Apr 2020 07:50:39: 6000000 INFO @ Wed, 22 Apr 2020 07:50:43: 10000000 INFO @ Wed, 22 Apr 2020 07:50:46: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:50:47: 7000000 INFO @ Wed, 22 Apr 2020 07:50:52: 11000000 INFO @ Wed, 22 Apr 2020 07:50:54: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 07:50:54: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 07:50:54: #1 total tags in treatment: 11314088 INFO @ Wed, 22 Apr 2020 07:50:54: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:50:54: #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 07:50:54: #1 tags after filtering in treatment: 11313891 INFO @ Wed, 22 Apr 2020 07:50:54: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:50:54: #1 finished! INFO @ Wed, 22 Apr 2020 07:50:54: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:50:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:50:55: 8000000 INFO @ Wed, 22 Apr 2020 07:50:56: #2 number of paired peaks: 5056 INFO @ Wed, 22 Apr 2020 07:50:56: start model_add_line... INFO @ Wed, 22 Apr 2020 07:50:56: start X-correlation... INFO @ Wed, 22 Apr 2020 07:50:56: end of X-cor INFO @ Wed, 22 Apr 2020 07:50:56: #2 finished! INFO @ Wed, 22 Apr 2020 07:50:56: #2 predicted fragment length is 73 bps INFO @ Wed, 22 Apr 2020 07:50:56: #2 alternative fragment length(s) may be 73 bps INFO @ Wed, 22 Apr 2020 07:50:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX7625167/SRX7625167.10_model.r WARNING @ Wed, 22 Apr 2020 07:50:56: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:50:56: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Wed, 22 Apr 2020 07:50:56: #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 07:50:56: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:50:56: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:50:59: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX7625167/SRX7625167.05_peaks.xls INFO @ Wed, 22 Apr 2020 07:50:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX7625167/SRX7625167.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:50:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX7625167/SRX7625167.05_summits.bed INFO @ Wed, 22 Apr 2020 07:50:59: Done! pass1 - making usageList (47 chroms): 1 millis pass2 - checking and writing primary data (807 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 07:51:03: 9000000 INFO @ Wed, 22 Apr 2020 07:51:11: 10000000 INFO @ Wed, 22 Apr 2020 07:51:19: 11000000 INFO @ Wed, 22 Apr 2020 07:51:21: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:51:21: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 07:51:21: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 07:51:21: #1 total tags in treatment: 11314088 INFO @ Wed, 22 Apr 2020 07:51:21: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:51:21: #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 07:51:22: #1 tags after filtering in treatment: 11313891 INFO @ Wed, 22 Apr 2020 07:51:22: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:51:22: #1 finished! INFO @ Wed, 22 Apr 2020 07:51:22: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:51:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:51:23: #2 number of paired peaks: 5056 INFO @ Wed, 22 Apr 2020 07:51:23: start model_add_line... INFO @ Wed, 22 Apr 2020 07:51:23: start X-correlation... INFO @ Wed, 22 Apr 2020 07:51:23: end of X-cor INFO @ Wed, 22 Apr 2020 07:51:23: #2 finished! INFO @ Wed, 22 Apr 2020 07:51:23: #2 predicted fragment length is 73 bps INFO @ Wed, 22 Apr 2020 07:51:23: #2 alternative fragment length(s) may be 73 bps INFO @ Wed, 22 Apr 2020 07:51:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX7625167/SRX7625167.20_model.r WARNING @ Wed, 22 Apr 2020 07:51:23: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:51:23: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Wed, 22 Apr 2020 07:51:23: #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 07:51:23: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:51:23: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:51:34: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX7625167/SRX7625167.10_peaks.xls INFO @ Wed, 22 Apr 2020 07:51:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX7625167/SRX7625167.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:51:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX7625167/SRX7625167.10_summits.bed INFO @ Wed, 22 Apr 2020 07:51:34: Done! pass1 - making usageList (40 chroms): 0 millis pass2 - checking and writing primary data (520 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 07:51:47: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:52:00: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX7625167/SRX7625167.20_peaks.xls INFO @ Wed, 22 Apr 2020 07:52:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX7625167/SRX7625167.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:52:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX7625167/SRX7625167.20_summits.bed INFO @ Wed, 22 Apr 2020 07:52:00: Done! pass1 - making usageList (28 chroms): 1 millis pass2 - checking and writing primary data (284 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。