Job ID = 5720956 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 11,920,596 reads read : 11,920,596 reads written : 11,920,596 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: 00:01:58 11920596 reads; of these: 11920596 (100.00%) were unpaired; of these: 8324835 (69.84%) aligned 0 times 2619812 (21.98%) aligned exactly 1 time 975949 (8.19%) aligned >1 times 30.16% overall alignment rate Time searching: 00:01:58 Overall time: 00:01:58 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] 1139537 / 3595761 = 0.3169 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 03:38:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386750/SRX6386750.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386750/SRX6386750.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386750/SRX6386750.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386750/SRX6386750.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 03:38:18: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:38:18: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:38:27: 1000000 INFO @ Thu, 16 Apr 2020 03:38:34: 2000000 INFO @ Thu, 16 Apr 2020 03:38:37: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 03:38:37: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 03:38:37: #1 total tags in treatment: 2456224 INFO @ Thu, 16 Apr 2020 03:38:37: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:38:37: #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 03:38:37: #1 tags after filtering in treatment: 2456224 INFO @ Thu, 16 Apr 2020 03:38:37: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:38:37: #1 finished! INFO @ Thu, 16 Apr 2020 03:38:37: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:38:37: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:38:38: #2 number of paired peaks: 133 WARNING @ Thu, 16 Apr 2020 03:38:38: Fewer paired peaks (133) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 133 pairs to build model! INFO @ Thu, 16 Apr 2020 03:38:38: start model_add_line... INFO @ Thu, 16 Apr 2020 03:38:38: start X-correlation... INFO @ Thu, 16 Apr 2020 03:38:38: end of X-cor INFO @ Thu, 16 Apr 2020 03:38:38: #2 finished! INFO @ Thu, 16 Apr 2020 03:38:38: #2 predicted fragment length is 50 bps INFO @ Thu, 16 Apr 2020 03:38:38: #2 alternative fragment length(s) may be 50 bps INFO @ Thu, 16 Apr 2020 03:38:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386750/SRX6386750.05_model.r WARNING @ Thu, 16 Apr 2020 03:38:38: #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 03:38:38: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Thu, 16 Apr 2020 03:38:38: #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 03:38:38: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:38:38: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:38:43: #3 Call peaks for each chromosome... 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 03:38:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386750/SRX6386750.05_peaks.xls INFO @ Thu, 16 Apr 2020 03:38:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386750/SRX6386750.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:38:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386750/SRX6386750.05_summits.bed INFO @ Thu, 16 Apr 2020 03:38:45: Done! INFO @ Thu, 16 Apr 2020 03:38:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386750/SRX6386750.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386750/SRX6386750.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386750/SRX6386750.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386750/SRX6386750.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 03:38:48: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:38:48: #1 read treatment tags... pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (354 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:38:54: 1000000 INFO @ Thu, 16 Apr 2020 03:39:00: 2000000 INFO @ Thu, 16 Apr 2020 03:39:03: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 03:39:03: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 03:39:03: #1 total tags in treatment: 2456224 INFO @ Thu, 16 Apr 2020 03:39:03: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:39:03: #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 03:39:03: #1 tags after filtering in treatment: 2456224 INFO @ Thu, 16 Apr 2020 03:39:03: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:39:03: #1 finished! INFO @ Thu, 16 Apr 2020 03:39:03: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:39:03: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:39:03: #2 number of paired peaks: 133 WARNING @ Thu, 16 Apr 2020 03:39:03: Fewer paired peaks (133) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 133 pairs to build model! INFO @ Thu, 16 Apr 2020 03:39:03: start model_add_line... INFO @ Thu, 16 Apr 2020 03:39:03: start X-correlation... INFO @ Thu, 16 Apr 2020 03:39:03: end of X-cor INFO @ Thu, 16 Apr 2020 03:39:03: #2 finished! INFO @ Thu, 16 Apr 2020 03:39:03: #2 predicted fragment length is 50 bps INFO @ Thu, 16 Apr 2020 03:39:03: #2 alternative fragment length(s) may be 50 bps INFO @ Thu, 16 Apr 2020 03:39:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386750/SRX6386750.10_model.r WARNING @ Thu, 16 Apr 2020 03:39:03: #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 03:39:03: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Thu, 16 Apr 2020 03:39:03: #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 03:39:03: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:39:03: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:39:08: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:39:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386750/SRX6386750.10_peaks.xls INFO @ Thu, 16 Apr 2020 03:39:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386750/SRX6386750.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:39:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386750/SRX6386750.10_summits.bed INFO @ Thu, 16 Apr 2020 03:39:11: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (159 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 03:39:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386750/SRX6386750.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386750/SRX6386750.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386750/SRX6386750.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386750/SRX6386750.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 03:39:18: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:39:18: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:39:24: 1000000 INFO @ Thu, 16 Apr 2020 03:39:30: 2000000 INFO @ Thu, 16 Apr 2020 03:39:33: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 03:39:33: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 03:39:33: #1 total tags in treatment: 2456224 INFO @ Thu, 16 Apr 2020 03:39:33: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:39:33: #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 03:39:33: #1 tags after filtering in treatment: 2456224 INFO @ Thu, 16 Apr 2020 03:39:33: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:39:33: #1 finished! INFO @ Thu, 16 Apr 2020 03:39:33: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:39:33: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:39:33: #2 number of paired peaks: 133 WARNING @ Thu, 16 Apr 2020 03:39:33: Fewer paired peaks (133) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 133 pairs to build model! INFO @ Thu, 16 Apr 2020 03:39:33: start model_add_line... INFO @ Thu, 16 Apr 2020 03:39:33: start X-correlation... INFO @ Thu, 16 Apr 2020 03:39:33: end of X-cor INFO @ Thu, 16 Apr 2020 03:39:33: #2 finished! INFO @ Thu, 16 Apr 2020 03:39:33: #2 predicted fragment length is 50 bps INFO @ Thu, 16 Apr 2020 03:39:33: #2 alternative fragment length(s) may be 50 bps INFO @ Thu, 16 Apr 2020 03:39:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386750/SRX6386750.20_model.r WARNING @ Thu, 16 Apr 2020 03:39:33: #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 03:39:33: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Thu, 16 Apr 2020 03:39:33: #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 03:39:33: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:39:33: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:39:38: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:39:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386750/SRX6386750.20_peaks.xls INFO @ Thu, 16 Apr 2020 03:39:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386750/SRX6386750.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:39:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386750/SRX6386750.20_summits.bed INFO @ Thu, 16 Apr 2020 03:39:41: Done! BedGraph に変換しました。 BigWig に変換中... pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (62 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。