Job ID = 5720765 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 11,293,501 reads read : 22,587,002 reads written : 11,293,501 reads 0-length : 11,293,501 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: 00:04:41 11293501 reads; of these: 11293501 (100.00%) were unpaired; of these: 541026 (4.79%) aligned 0 times 7861076 (69.61%) aligned exactly 1 time 2891399 (25.60%) aligned >1 times 95.21% overall alignment rate Time searching: 00:04:41 Overall time: 00:04:41 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] 866311 / 10752475 = 0.0806 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 01:29:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5227002/SRX5227002.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5227002/SRX5227002.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5227002/SRX5227002.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5227002/SRX5227002.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 01:29:11: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:29:11: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:29:17: 1000000 INFO @ Thu, 16 Apr 2020 01:29:23: 2000000 INFO @ Thu, 16 Apr 2020 01:29:29: 3000000 INFO @ Thu, 16 Apr 2020 01:29:35: 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 @ Thu, 16 Apr 2020 01:29:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5227002/SRX5227002.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5227002/SRX5227002.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5227002/SRX5227002.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5227002/SRX5227002.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 01:29:41: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:29:41: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:29:41: 5000000 INFO @ Thu, 16 Apr 2020 01:29:48: 1000000 INFO @ Thu, 16 Apr 2020 01:29:48: 6000000 INFO @ Thu, 16 Apr 2020 01:29:55: 2000000 INFO @ Thu, 16 Apr 2020 01:29:55: 7000000 INFO @ Thu, 16 Apr 2020 01:30:02: 8000000 INFO @ Thu, 16 Apr 2020 01:30:02: 3000000 INFO @ Thu, 16 Apr 2020 01:30:09: 9000000 INFO @ Thu, 16 Apr 2020 01:30:09: 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 @ Thu, 16 Apr 2020 01:30:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5227002/SRX5227002.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5227002/SRX5227002.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5227002/SRX5227002.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5227002/SRX5227002.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 01:30:11: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:30:11: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:30:15: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:30:15: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:30:15: #1 total tags in treatment: 9886164 INFO @ Thu, 16 Apr 2020 01:30:15: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:30:15: #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 01:30:15: #1 tags after filtering in treatment: 9886164 INFO @ Thu, 16 Apr 2020 01:30:15: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:30:15: #1 finished! INFO @ Thu, 16 Apr 2020 01:30:15: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:30:15: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:30:16: #2 number of paired peaks: 742 WARNING @ Thu, 16 Apr 2020 01:30:16: Fewer paired peaks (742) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 742 pairs to build model! INFO @ Thu, 16 Apr 2020 01:30:16: start model_add_line... INFO @ Thu, 16 Apr 2020 01:30:16: start X-correlation... INFO @ Thu, 16 Apr 2020 01:30:16: end of X-cor INFO @ Thu, 16 Apr 2020 01:30:16: #2 finished! INFO @ Thu, 16 Apr 2020 01:30:16: #2 predicted fragment length is 86 bps INFO @ Thu, 16 Apr 2020 01:30:16: #2 alternative fragment length(s) may be 86 bps INFO @ Thu, 16 Apr 2020 01:30:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5227002/SRX5227002.05_model.r WARNING @ Thu, 16 Apr 2020 01:30:16: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:30:16: #2 You may need to consider one of the other alternative d(s): 86 WARNING @ Thu, 16 Apr 2020 01:30:16: #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 01:30:16: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:30:16: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:30:16: 5000000 INFO @ Thu, 16 Apr 2020 01:30:19: 1000000 INFO @ Thu, 16 Apr 2020 01:30:24: 6000000 INFO @ Thu, 16 Apr 2020 01:30:26: 2000000 INFO @ Thu, 16 Apr 2020 01:30:31: 7000000 INFO @ Thu, 16 Apr 2020 01:30:34: 3000000 INFO @ Thu, 16 Apr 2020 01:30:36: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:30:38: 8000000 INFO @ Thu, 16 Apr 2020 01:30:41: 4000000 INFO @ Thu, 16 Apr 2020 01:30:44: 9000000 INFO @ Thu, 16 Apr 2020 01:30:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5227002/SRX5227002.05_peaks.xls INFO @ Thu, 16 Apr 2020 01:30:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5227002/SRX5227002.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:30:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5227002/SRX5227002.05_summits.bed INFO @ Thu, 16 Apr 2020 01:30:46: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3639 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:30:48: 5000000 INFO @ Thu, 16 Apr 2020 01:30:50: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:30:50: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:30:50: #1 total tags in treatment: 9886164 INFO @ Thu, 16 Apr 2020 01:30:50: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:30:50: #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 01:30:51: #1 tags after filtering in treatment: 9886164 INFO @ Thu, 16 Apr 2020 01:30:51: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:30:51: #1 finished! INFO @ Thu, 16 Apr 2020 01:30:51: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:30:51: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:30:51: #2 number of paired peaks: 742 WARNING @ Thu, 16 Apr 2020 01:30:51: Fewer paired peaks (742) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 742 pairs to build model! INFO @ Thu, 16 Apr 2020 01:30:51: start model_add_line... INFO @ Thu, 16 Apr 2020 01:30:51: start X-correlation... INFO @ Thu, 16 Apr 2020 01:30:51: end of X-cor INFO @ Thu, 16 Apr 2020 01:30:51: #2 finished! INFO @ Thu, 16 Apr 2020 01:30:51: #2 predicted fragment length is 86 bps INFO @ Thu, 16 Apr 2020 01:30:51: #2 alternative fragment length(s) may be 86 bps INFO @ Thu, 16 Apr 2020 01:30:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5227002/SRX5227002.10_model.r WARNING @ Thu, 16 Apr 2020 01:30:51: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:30:51: #2 You may need to consider one of the other alternative d(s): 86 WARNING @ Thu, 16 Apr 2020 01:30:51: #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 01:30:51: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:30:51: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:30:54: 6000000 INFO @ Thu, 16 Apr 2020 01:31:01: 7000000 INFO @ Thu, 16 Apr 2020 01:31:08: 8000000 INFO @ Thu, 16 Apr 2020 01:31:11: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:31:14: 9000000 INFO @ Thu, 16 Apr 2020 01:31:20: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:31:20: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:31:20: #1 total tags in treatment: 9886164 INFO @ Thu, 16 Apr 2020 01:31:20: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:31:20: #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 01:31:20: #1 tags after filtering in treatment: 9886164 INFO @ Thu, 16 Apr 2020 01:31:20: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:31:20: #1 finished! INFO @ Thu, 16 Apr 2020 01:31:20: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:31:20: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:31:20: #2 number of paired peaks: 742 WARNING @ Thu, 16 Apr 2020 01:31:20: Fewer paired peaks (742) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 742 pairs to build model! INFO @ Thu, 16 Apr 2020 01:31:20: start model_add_line... INFO @ Thu, 16 Apr 2020 01:31:20: start X-correlation... INFO @ Thu, 16 Apr 2020 01:31:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5227002/SRX5227002.10_peaks.xls INFO @ Thu, 16 Apr 2020 01:31:21: end of X-cor INFO @ Thu, 16 Apr 2020 01:31:21: #2 finished! INFO @ Thu, 16 Apr 2020 01:31:21: #2 predicted fragment length is 86 bps INFO @ Thu, 16 Apr 2020 01:31:21: #2 alternative fragment length(s) may be 86 bps INFO @ Thu, 16 Apr 2020 01:31:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5227002/SRX5227002.20_model.r WARNING @ Thu, 16 Apr 2020 01:31:21: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:31:21: #2 You may need to consider one of the other alternative d(s): 86 WARNING @ Thu, 16 Apr 2020 01:31:21: #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 01:31:21: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:31:21: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:31:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5227002/SRX5227002.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:31:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5227002/SRX5227002.10_summits.bed INFO @ Thu, 16 Apr 2020 01:31:21: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1746 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:31:42: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:31:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5227002/SRX5227002.20_peaks.xls INFO @ Thu, 16 Apr 2020 01:31:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5227002/SRX5227002.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:31:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5227002/SRX5227002.20_summits.bed INFO @ Thu, 16 Apr 2020 01:31:53: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (681 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。