Job ID = 5721037 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,770,252 reads read : 18,770,252 reads written : 18,770,252 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:57 18770252 reads; of these: 18770252 (100.00%) were unpaired; of these: 3099268 (16.51%) aligned 0 times 7284476 (38.81%) aligned exactly 1 time 8386508 (44.68%) aligned >1 times 83.49% overall alignment rate Time searching: 00:04:57 Overall time: 00:04:57 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_sort_core] merging from 8 files... [bam_rmdupse_core] 10870416 / 15670984 = 0.6937 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 03:49:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386772/SRX6386772.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386772/SRX6386772.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386772/SRX6386772.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386772/SRX6386772.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 03:49:43: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:49:43: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:49:48: 1000000 INFO @ Thu, 16 Apr 2020 03:49:52: 2000000 INFO @ Thu, 16 Apr 2020 03:49:57: 3000000 INFO @ Thu, 16 Apr 2020 03:50:02: 4000000 INFO @ Thu, 16 Apr 2020 03:50:05: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 03:50:05: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 03:50:05: #1 total tags in treatment: 4800568 INFO @ Thu, 16 Apr 2020 03:50:05: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:50:05: #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 03:50:06: #1 tags after filtering in treatment: 4800568 INFO @ Thu, 16 Apr 2020 03:50:06: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:50:06: #1 finished! INFO @ Thu, 16 Apr 2020 03:50:06: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:50:06: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:50:06: #2 number of paired peaks: 624 WARNING @ Thu, 16 Apr 2020 03:50:06: 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 03:50:06: start model_add_line... INFO @ Thu, 16 Apr 2020 03:50:06: start X-correlation... INFO @ Thu, 16 Apr 2020 03:50:06: end of X-cor INFO @ Thu, 16 Apr 2020 03:50:06: #2 finished! INFO @ Thu, 16 Apr 2020 03:50:06: #2 predicted fragment length is 50 bps INFO @ Thu, 16 Apr 2020 03:50:06: #2 alternative fragment length(s) may be 50 bps INFO @ Thu, 16 Apr 2020 03:50:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386772/SRX6386772.05_model.r WARNING @ Thu, 16 Apr 2020 03:50:06: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:50:06: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Thu, 16 Apr 2020 03:50:06: #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 03:50:06: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:50:06: #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 03:50:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386772/SRX6386772.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386772/SRX6386772.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386772/SRX6386772.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386772/SRX6386772.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 03:50:13: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:50:13: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:50:16: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:50:19: 1000000 INFO @ Thu, 16 Apr 2020 03:50:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386772/SRX6386772.05_peaks.xls INFO @ Thu, 16 Apr 2020 03:50:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386772/SRX6386772.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:50:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386772/SRX6386772.05_summits.bed INFO @ Thu, 16 Apr 2020 03:50:21: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1438 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:50:24: 2000000 INFO @ Thu, 16 Apr 2020 03:50:30: 3000000 INFO @ Thu, 16 Apr 2020 03:50:35: 4000000 INFO @ Thu, 16 Apr 2020 03:50:39: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 03:50:39: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 03:50:39: #1 total tags in treatment: 4800568 INFO @ Thu, 16 Apr 2020 03:50:39: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:50:39: #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 03:50:40: #1 tags after filtering in treatment: 4800568 INFO @ Thu, 16 Apr 2020 03:50:40: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:50:40: #1 finished! INFO @ Thu, 16 Apr 2020 03:50:40: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:50:40: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:50:40: #2 number of paired peaks: 624 WARNING @ Thu, 16 Apr 2020 03:50:40: 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 03:50:40: start model_add_line... INFO @ Thu, 16 Apr 2020 03:50:40: start X-correlation... INFO @ Thu, 16 Apr 2020 03:50:40: end of X-cor INFO @ Thu, 16 Apr 2020 03:50:40: #2 finished! INFO @ Thu, 16 Apr 2020 03:50:40: #2 predicted fragment length is 50 bps INFO @ Thu, 16 Apr 2020 03:50:40: #2 alternative fragment length(s) may be 50 bps INFO @ Thu, 16 Apr 2020 03:50:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386772/SRX6386772.10_model.r WARNING @ Thu, 16 Apr 2020 03:50:40: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:50:40: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Thu, 16 Apr 2020 03:50:40: #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 03:50:40: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:50:40: #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 03:50:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386772/SRX6386772.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386772/SRX6386772.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386772/SRX6386772.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386772/SRX6386772.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 03:50:43: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:50:43: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:50:48: 1000000 INFO @ Thu, 16 Apr 2020 03:50:50: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:50:52: 2000000 INFO @ Thu, 16 Apr 2020 03:50:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386772/SRX6386772.10_peaks.xls INFO @ Thu, 16 Apr 2020 03:50:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386772/SRX6386772.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:50:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386772/SRX6386772.10_summits.bed INFO @ Thu, 16 Apr 2020 03:50:55: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (1129 records, 4 fields): 3 millis INFO @ Thu, 16 Apr 2020 03:50:57: 3000000 INFO @ Thu, 16 Apr 2020 03:51:02: 4000000 CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:51:06: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 03:51:06: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 03:51:06: #1 total tags in treatment: 4800568 INFO @ Thu, 16 Apr 2020 03:51:06: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:51:06: #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 03:51:06: #1 tags after filtering in treatment: 4800568 INFO @ Thu, 16 Apr 2020 03:51:06: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:51:06: #1 finished! INFO @ Thu, 16 Apr 2020 03:51:06: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:51:06: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:51:06: #2 number of paired peaks: 624 WARNING @ Thu, 16 Apr 2020 03:51:06: 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 03:51:06: start model_add_line... INFO @ Thu, 16 Apr 2020 03:51:06: start X-correlation... INFO @ Thu, 16 Apr 2020 03:51:06: end of X-cor INFO @ Thu, 16 Apr 2020 03:51:06: #2 finished! INFO @ Thu, 16 Apr 2020 03:51:06: #2 predicted fragment length is 50 bps INFO @ Thu, 16 Apr 2020 03:51:06: #2 alternative fragment length(s) may be 50 bps INFO @ Thu, 16 Apr 2020 03:51:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386772/SRX6386772.20_model.r WARNING @ Thu, 16 Apr 2020 03:51:06: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:51:06: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Thu, 16 Apr 2020 03:51:06: #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 03:51:06: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:51:06: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:51:16: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:51:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386772/SRX6386772.20_peaks.xls INFO @ Thu, 16 Apr 2020 03:51:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386772/SRX6386772.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:51:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386772/SRX6386772.20_summits.bed INFO @ Thu, 16 Apr 2020 03:51:21: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (731 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。