Job ID = 5720599 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 9,724,038 reads read : 9,724,038 reads written : 9,724,038 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289723.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: 00:03:15 9724038 reads; of these: 9724038 (100.00%) were unpaired; of these: 1261942 (12.98%) aligned 0 times 6482044 (66.66%) aligned exactly 1 time 1980052 (20.36%) aligned >1 times 87.02% overall alignment rate Time searching: 00:03:15 Overall time: 00:03:15 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 1889858 / 8462096 = 0.2233 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 00:46:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592446/SRX2592446.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592446/SRX2592446.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592446/SRX2592446.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592446/SRX2592446.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 00:46:46: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:46:46: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:46:52: 1000000 INFO @ Thu, 16 Apr 2020 00:46:59: 2000000 INFO @ Thu, 16 Apr 2020 00:47:06: 3000000 INFO @ Thu, 16 Apr 2020 00:47:13: 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 00:47:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592446/SRX2592446.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592446/SRX2592446.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592446/SRX2592446.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592446/SRX2592446.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 00:47:16: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:47:16: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:47:20: 5000000 INFO @ Thu, 16 Apr 2020 00:47:24: 1000000 INFO @ Thu, 16 Apr 2020 00:47:27: 6000000 INFO @ Thu, 16 Apr 2020 00:47:31: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:47:31: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:47:31: #1 total tags in treatment: 6572238 INFO @ Thu, 16 Apr 2020 00:47:31: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:47:31: #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 00:47:32: #1 tags after filtering in treatment: 6572238 INFO @ Thu, 16 Apr 2020 00:47:32: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:47:32: #1 finished! INFO @ Thu, 16 Apr 2020 00:47:32: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:47:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:47:32: 2000000 INFO @ Thu, 16 Apr 2020 00:47:32: #2 number of paired peaks: 212 WARNING @ Thu, 16 Apr 2020 00:47:32: Fewer paired peaks (212) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 212 pairs to build model! INFO @ Thu, 16 Apr 2020 00:47:32: start model_add_line... INFO @ Thu, 16 Apr 2020 00:47:32: start X-correlation... INFO @ Thu, 16 Apr 2020 00:47:32: end of X-cor INFO @ Thu, 16 Apr 2020 00:47:32: #2 finished! INFO @ Thu, 16 Apr 2020 00:47:32: #2 predicted fragment length is 90 bps INFO @ Thu, 16 Apr 2020 00:47:32: #2 alternative fragment length(s) may be 90 bps INFO @ Thu, 16 Apr 2020 00:47:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592446/SRX2592446.05_model.r WARNING @ Thu, 16 Apr 2020 00:47:32: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:47:32: #2 You may need to consider one of the other alternative d(s): 90 WARNING @ Thu, 16 Apr 2020 00:47:32: #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 00:47:32: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:47:32: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:47:39: 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 @ Thu, 16 Apr 2020 00:47:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592446/SRX2592446.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592446/SRX2592446.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592446/SRX2592446.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592446/SRX2592446.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 00:47:46: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:47:46: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:47:46: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:47:46: 4000000 INFO @ Thu, 16 Apr 2020 00:47:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592446/SRX2592446.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:47:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592446/SRX2592446.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:47:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592446/SRX2592446.05_summits.bed INFO @ Thu, 16 Apr 2020 00:47:53: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6364 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:47:54: 1000000 INFO @ Thu, 16 Apr 2020 00:47:54: 5000000 INFO @ Thu, 16 Apr 2020 00:48:01: 2000000 INFO @ Thu, 16 Apr 2020 00:48:02: 6000000 INFO @ Thu, 16 Apr 2020 00:48:06: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:48:06: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:48:06: #1 total tags in treatment: 6572238 INFO @ Thu, 16 Apr 2020 00:48:06: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:48:06: #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 00:48:06: #1 tags after filtering in treatment: 6572238 INFO @ Thu, 16 Apr 2020 00:48:06: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:48:06: #1 finished! INFO @ Thu, 16 Apr 2020 00:48:06: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:48:06: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:48:06: #2 number of paired peaks: 212 WARNING @ Thu, 16 Apr 2020 00:48:06: Fewer paired peaks (212) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 212 pairs to build model! INFO @ Thu, 16 Apr 2020 00:48:06: start model_add_line... INFO @ Thu, 16 Apr 2020 00:48:07: start X-correlation... INFO @ Thu, 16 Apr 2020 00:48:07: end of X-cor INFO @ Thu, 16 Apr 2020 00:48:07: #2 finished! INFO @ Thu, 16 Apr 2020 00:48:07: #2 predicted fragment length is 90 bps INFO @ Thu, 16 Apr 2020 00:48:07: #2 alternative fragment length(s) may be 90 bps INFO @ Thu, 16 Apr 2020 00:48:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592446/SRX2592446.10_model.r WARNING @ Thu, 16 Apr 2020 00:48:07: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:48:07: #2 You may need to consider one of the other alternative d(s): 90 WARNING @ Thu, 16 Apr 2020 00:48:07: #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 00:48:07: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:48:07: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:48:09: 3000000 INFO @ Thu, 16 Apr 2020 00:48:16: 4000000 INFO @ Thu, 16 Apr 2020 00:48:21: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:48:23: 5000000 INFO @ Thu, 16 Apr 2020 00:48:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592446/SRX2592446.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:48:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592446/SRX2592446.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:48:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592446/SRX2592446.10_summits.bed INFO @ Thu, 16 Apr 2020 00:48:29: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2853 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:48:30: 6000000 INFO @ Thu, 16 Apr 2020 00:48:34: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:48:34: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:48:34: #1 total tags in treatment: 6572238 INFO @ Thu, 16 Apr 2020 00:48:34: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:48:34: #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 00:48:34: #1 tags after filtering in treatment: 6572238 INFO @ Thu, 16 Apr 2020 00:48:34: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:48:34: #1 finished! INFO @ Thu, 16 Apr 2020 00:48:34: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:48:34: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:48:35: #2 number of paired peaks: 212 WARNING @ Thu, 16 Apr 2020 00:48:35: Fewer paired peaks (212) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 212 pairs to build model! INFO @ Thu, 16 Apr 2020 00:48:35: start model_add_line... INFO @ Thu, 16 Apr 2020 00:48:35: start X-correlation... INFO @ Thu, 16 Apr 2020 00:48:35: end of X-cor INFO @ Thu, 16 Apr 2020 00:48:35: #2 finished! INFO @ Thu, 16 Apr 2020 00:48:35: #2 predicted fragment length is 90 bps INFO @ Thu, 16 Apr 2020 00:48:35: #2 alternative fragment length(s) may be 90 bps INFO @ Thu, 16 Apr 2020 00:48:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592446/SRX2592446.20_model.r WARNING @ Thu, 16 Apr 2020 00:48:35: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:48:35: #2 You may need to consider one of the other alternative d(s): 90 WARNING @ Thu, 16 Apr 2020 00:48:35: #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 00:48:35: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:48:35: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:48:50: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:48:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592446/SRX2592446.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:48:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592446/SRX2592446.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:48:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592446/SRX2592446.20_summits.bed INFO @ Thu, 16 Apr 2020 00:48:58: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (605 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。