Job ID = 5720661 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 12,337,626 reads read : 12,337,626 reads written : 12,337,626 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289757.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 12337626 reads; of these: 12337626 (100.00%) were unpaired; of these: 3785823 (30.69%) aligned 0 times 6231158 (50.51%) aligned exactly 1 time 2320645 (18.81%) aligned >1 times 69.31% 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] 770290 / 8551803 = 0.0901 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 00:55:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592480/SRX2592480.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592480/SRX2592480.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592480/SRX2592480.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592480/SRX2592480.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 00:55:30: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:55:30: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:55:36: 1000000 INFO @ Thu, 16 Apr 2020 00:55:42: 2000000 INFO @ Thu, 16 Apr 2020 00:55:49: 3000000 INFO @ Thu, 16 Apr 2020 00:55:56: 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 00:56:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592480/SRX2592480.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592480/SRX2592480.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592480/SRX2592480.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592480/SRX2592480.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 00:56:00: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:56:00: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:56:02: 5000000 INFO @ Thu, 16 Apr 2020 00:56:06: 1000000 INFO @ Thu, 16 Apr 2020 00:56:08: 6000000 INFO @ Thu, 16 Apr 2020 00:56:12: 2000000 INFO @ Thu, 16 Apr 2020 00:56:14: 7000000 INFO @ Thu, 16 Apr 2020 00:56:18: 3000000 INFO @ Thu, 16 Apr 2020 00:56:18: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:56:18: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:56:18: #1 total tags in treatment: 7781513 INFO @ Thu, 16 Apr 2020 00:56:18: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:56:18: #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 00:56:18: #1 tags after filtering in treatment: 7781513 INFO @ Thu, 16 Apr 2020 00:56:18: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:56:18: #1 finished! INFO @ Thu, 16 Apr 2020 00:56:18: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:56:18: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:56:19: #2 number of paired peaks: 358 WARNING @ Thu, 16 Apr 2020 00:56:19: Fewer paired peaks (358) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 358 pairs to build model! INFO @ Thu, 16 Apr 2020 00:56:19: start model_add_line... INFO @ Thu, 16 Apr 2020 00:56:19: start X-correlation... INFO @ Thu, 16 Apr 2020 00:56:19: end of X-cor INFO @ Thu, 16 Apr 2020 00:56:19: #2 finished! INFO @ Thu, 16 Apr 2020 00:56:19: #2 predicted fragment length is 52 bps INFO @ Thu, 16 Apr 2020 00:56:19: #2 alternative fragment length(s) may be 52 bps INFO @ Thu, 16 Apr 2020 00:56:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592480/SRX2592480.05_model.r WARNING @ Thu, 16 Apr 2020 00:56:19: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:56:19: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Thu, 16 Apr 2020 00:56:19: #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 00:56:19: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:56:19: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:56:23: 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 00:56:29: 5000000 INFO @ Thu, 16 Apr 2020 00:56:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592480/SRX2592480.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592480/SRX2592480.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592480/SRX2592480.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592480/SRX2592480.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 00:56:30: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:56:30: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:56:34: 6000000 INFO @ Thu, 16 Apr 2020 00:56:35: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:56:36: 1000000 INFO @ Thu, 16 Apr 2020 00:56:40: 7000000 INFO @ Thu, 16 Apr 2020 00:56:41: 2000000 INFO @ Thu, 16 Apr 2020 00:56:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592480/SRX2592480.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:56:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592480/SRX2592480.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:56:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592480/SRX2592480.05_summits.bed INFO @ Thu, 16 Apr 2020 00:56:42: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1421 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:56:44: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:56:44: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:56:44: #1 total tags in treatment: 7781513 INFO @ Thu, 16 Apr 2020 00:56:44: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:56:44: #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 00:56:44: #1 tags after filtering in treatment: 7781513 INFO @ Thu, 16 Apr 2020 00:56:44: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:56:44: #1 finished! INFO @ Thu, 16 Apr 2020 00:56:44: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:56:44: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:56:45: #2 number of paired peaks: 358 WARNING @ Thu, 16 Apr 2020 00:56:45: Fewer paired peaks (358) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 358 pairs to build model! INFO @ Thu, 16 Apr 2020 00:56:45: start model_add_line... INFO @ Thu, 16 Apr 2020 00:56:45: start X-correlation... INFO @ Thu, 16 Apr 2020 00:56:45: end of X-cor INFO @ Thu, 16 Apr 2020 00:56:45: #2 finished! INFO @ Thu, 16 Apr 2020 00:56:45: #2 predicted fragment length is 52 bps INFO @ Thu, 16 Apr 2020 00:56:45: #2 alternative fragment length(s) may be 52 bps INFO @ Thu, 16 Apr 2020 00:56:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592480/SRX2592480.10_model.r WARNING @ Thu, 16 Apr 2020 00:56:45: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:56:45: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Thu, 16 Apr 2020 00:56:45: #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 00:56:45: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:56:45: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:56:47: 3000000 INFO @ Thu, 16 Apr 2020 00:56:52: 4000000 INFO @ Thu, 16 Apr 2020 00:56:57: 5000000 INFO @ Thu, 16 Apr 2020 00:57:01: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:57:03: 6000000 INFO @ Thu, 16 Apr 2020 00:57:08: 7000000 INFO @ Thu, 16 Apr 2020 00:57:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592480/SRX2592480.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:57:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592480/SRX2592480.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:57:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592480/SRX2592480.10_summits.bed INFO @ Thu, 16 Apr 2020 00:57:09: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (978 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:57:12: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:57:12: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:57:12: #1 total tags in treatment: 7781513 INFO @ Thu, 16 Apr 2020 00:57:12: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:57:12: #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 00:57:12: #1 tags after filtering in treatment: 7781513 INFO @ Thu, 16 Apr 2020 00:57:12: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:57:12: #1 finished! INFO @ Thu, 16 Apr 2020 00:57:12: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:57:12: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:57:12: #2 number of paired peaks: 358 WARNING @ Thu, 16 Apr 2020 00:57:12: Fewer paired peaks (358) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 358 pairs to build model! INFO @ Thu, 16 Apr 2020 00:57:12: start model_add_line... INFO @ Thu, 16 Apr 2020 00:57:12: start X-correlation... INFO @ Thu, 16 Apr 2020 00:57:12: end of X-cor INFO @ Thu, 16 Apr 2020 00:57:12: #2 finished! INFO @ Thu, 16 Apr 2020 00:57:12: #2 predicted fragment length is 52 bps INFO @ Thu, 16 Apr 2020 00:57:12: #2 alternative fragment length(s) may be 52 bps INFO @ Thu, 16 Apr 2020 00:57:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592480/SRX2592480.20_model.r WARNING @ Thu, 16 Apr 2020 00:57:12: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:57:12: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Thu, 16 Apr 2020 00:57:12: #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 00:57:12: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:57:12: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:57:28: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:57:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592480/SRX2592480.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:57:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592480/SRX2592480.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:57:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592480/SRX2592480.20_summits.bed INFO @ Thu, 16 Apr 2020 00:57:35: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (620 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。