Job ID = 5720885 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T17:47:03 fasterq-dump.2.9.6 fatal: SIGNAL - Segmentation fault spots read : 21,589,054 reads read : 21,589,054 reads written : 21,589,054 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR8997116.sra.cache’: 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:08 21589054 reads; of these: 21589054 (100.00%) were unpaired; of these: 14577041 (67.52%) aligned 0 times 4824974 (22.35%) aligned exactly 1 time 2187039 (10.13%) aligned >1 times 32.48% overall alignment rate Time searching: 00:05:08 Overall time: 00:05:08 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 2277866 / 7012013 = 0.3249 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 @ Thu, 16 Apr 2020 02:57:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5775913/SRX5775913.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5775913/SRX5775913.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5775913/SRX5775913.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5775913/SRX5775913.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 16 Apr 2020 02:57:09: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:57:09: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:57:14: 1000000 INFO @ Thu, 16 Apr 2020 02:57:20: 2000000 INFO @ Thu, 16 Apr 2020 02:57:25: 3000000 INFO @ Thu, 16 Apr 2020 02:57:30: 4000000 INFO @ Thu, 16 Apr 2020 02:57:34: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 02:57:34: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 02:57:34: #1 total tags in treatment: 4734147 INFO @ Thu, 16 Apr 2020 02:57:34: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:57:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 02:57:34: #1 tags after filtering in treatment: 4734147 INFO @ Thu, 16 Apr 2020 02:57:34: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 02:57:34: #1 finished! INFO @ Thu, 16 Apr 2020 02:57:34: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:57:34: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:57:34: #2 number of paired peaks: 624 WARNING @ Thu, 16 Apr 2020 02:57:34: Fewer paired peaks (624) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 624 pairs to build model! INFO @ Thu, 16 Apr 2020 02:57:34: start model_add_line... INFO @ Thu, 16 Apr 2020 02:57:34: start X-correlation... INFO @ Thu, 16 Apr 2020 02:57:35: end of X-cor INFO @ Thu, 16 Apr 2020 02:57:35: #2 finished! INFO @ Thu, 16 Apr 2020 02:57:35: #2 predicted fragment length is 74 bps INFO @ Thu, 16 Apr 2020 02:57:35: #2 alternative fragment length(s) may be 74 bps INFO @ Thu, 16 Apr 2020 02:57:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5775913/SRX5775913.05_model.r WARNING @ Thu, 16 Apr 2020 02:57:35: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 02:57:35: #2 You may need to consider one of the other alternative d(s): 74 WARNING @ Thu, 16 Apr 2020 02:57:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 02:57:35: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:57:35: #3 Pre-compute pvalue-qvalue table... 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 @ Thu, 16 Apr 2020 02:57:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5775913/SRX5775913.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5775913/SRX5775913.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5775913/SRX5775913.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5775913/SRX5775913.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 16 Apr 2020 02:57:39: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:57:39: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:57:44: 1000000 INFO @ Thu, 16 Apr 2020 02:57:45: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:57:49: 2000000 INFO @ Thu, 16 Apr 2020 02:57:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5775913/SRX5775913.05_peaks.xls INFO @ Thu, 16 Apr 2020 02:57:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5775913/SRX5775913.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:57:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5775913/SRX5775913.05_summits.bed INFO @ Thu, 16 Apr 2020 02:57:50: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2264 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 02:57:55: 3000000 INFO @ Thu, 16 Apr 2020 02:58:00: 4000000 INFO @ Thu, 16 Apr 2020 02:58:04: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 02:58:04: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 02:58:04: #1 total tags in treatment: 4734147 INFO @ Thu, 16 Apr 2020 02:58:04: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:58:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 02:58:04: #1 tags after filtering in treatment: 4734147 INFO @ Thu, 16 Apr 2020 02:58:04: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 02:58:04: #1 finished! INFO @ Thu, 16 Apr 2020 02:58:04: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:58:04: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:58:04: #2 number of paired peaks: 624 WARNING @ Thu, 16 Apr 2020 02:58:04: Fewer paired peaks (624) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 624 pairs to build model! INFO @ Thu, 16 Apr 2020 02:58:04: start model_add_line... INFO @ Thu, 16 Apr 2020 02:58:04: start X-correlation... INFO @ Thu, 16 Apr 2020 02:58:04: end of X-cor INFO @ Thu, 16 Apr 2020 02:58:04: #2 finished! INFO @ Thu, 16 Apr 2020 02:58:04: #2 predicted fragment length is 74 bps INFO @ Thu, 16 Apr 2020 02:58:04: #2 alternative fragment length(s) may be 74 bps INFO @ Thu, 16 Apr 2020 02:58:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5775913/SRX5775913.10_model.r WARNING @ Thu, 16 Apr 2020 02:58:04: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 02:58:04: #2 You may need to consider one of the other alternative d(s): 74 WARNING @ Thu, 16 Apr 2020 02:58:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 02:58:04: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:58:04: #3 Pre-compute pvalue-qvalue table... 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 @ Thu, 16 Apr 2020 02:58:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5775913/SRX5775913.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5775913/SRX5775913.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5775913/SRX5775913.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5775913/SRX5775913.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 16 Apr 2020 02:58:08: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:58:08: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:58:13: 1000000 INFO @ Thu, 16 Apr 2020 02:58:14: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:58:18: 2000000 INFO @ Thu, 16 Apr 2020 02:58:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5775913/SRX5775913.10_peaks.xls INFO @ Thu, 16 Apr 2020 02:58:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5775913/SRX5775913.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:58:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5775913/SRX5775913.10_summits.bed INFO @ Thu, 16 Apr 2020 02:58:20: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1281 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 02:58:24: 3000000 INFO @ Thu, 16 Apr 2020 02:58:29: 4000000 INFO @ Thu, 16 Apr 2020 02:58:33: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 02:58:33: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 02:58:33: #1 total tags in treatment: 4734147 INFO @ Thu, 16 Apr 2020 02:58:33: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:58:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 02:58:33: #1 tags after filtering in treatment: 4734147 INFO @ Thu, 16 Apr 2020 02:58:33: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 02:58:33: #1 finished! INFO @ Thu, 16 Apr 2020 02:58:33: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:58:33: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:58:33: #2 number of paired peaks: 624 WARNING @ Thu, 16 Apr 2020 02:58:33: Fewer paired peaks (624) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 624 pairs to build model! INFO @ Thu, 16 Apr 2020 02:58:33: start model_add_line... INFO @ Thu, 16 Apr 2020 02:58:33: start X-correlation... INFO @ Thu, 16 Apr 2020 02:58:33: end of X-cor INFO @ Thu, 16 Apr 2020 02:58:33: #2 finished! INFO @ Thu, 16 Apr 2020 02:58:33: #2 predicted fragment length is 74 bps INFO @ Thu, 16 Apr 2020 02:58:33: #2 alternative fragment length(s) may be 74 bps INFO @ Thu, 16 Apr 2020 02:58:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5775913/SRX5775913.20_model.r WARNING @ Thu, 16 Apr 2020 02:58:33: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 02:58:33: #2 You may need to consider one of the other alternative d(s): 74 WARNING @ Thu, 16 Apr 2020 02:58:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 02:58:33: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:58:33: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:58:43: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:58:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5775913/SRX5775913.20_peaks.xls INFO @ Thu, 16 Apr 2020 02:58:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5775913/SRX5775913.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:58:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5775913/SRX5775913.20_summits.bed INFO @ Thu, 16 Apr 2020 02:58:49: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (655 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。