Job ID = 6453512 SRX = SRX124477 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:52:04 prefetch.2.10.7: 1) Downloading 'SRR423933'... 2020-06-21T08:52:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:53:15 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:53:15 prefetch.2.10.7: 'SRR423933' is valid 2020-06-21T08:53:15 prefetch.2.10.7: 1) 'SRR423933' was downloaded successfully Read 4950487 spots for SRR423933/SRR423933.sra Written 4950487 spots for SRR423933/SRR423933.sra 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: 00:00:58 4950487 reads; of these: 4950487 (100.00%) were unpaired; of these: 256214 (5.18%) aligned 0 times 3507834 (70.86%) aligned exactly 1 time 1186439 (23.97%) aligned >1 times 94.82% overall alignment rate Time searching: 00:00:58 Overall time: 00:00:58 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_rmdupse_core] 277610 / 4694273 = 0.0591 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 @ Sun, 21 Jun 2020 17:55:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX124477/SRX124477.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX124477/SRX124477.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX124477/SRX124477.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX124477/SRX124477.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 @ Sun, 21 Jun 2020 17:55:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:55:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:56:03: 1000000 INFO @ Sun, 21 Jun 2020 17:56:09: 2000000 INFO @ Sun, 21 Jun 2020 17:56:15: 3000000 INFO @ Sun, 21 Jun 2020 17:56:21: 4000000 INFO @ Sun, 21 Jun 2020 17:56:24: #1 tag size is determined as 30 bps INFO @ Sun, 21 Jun 2020 17:56:24: #1 tag size = 30 INFO @ Sun, 21 Jun 2020 17:56:24: #1 total tags in treatment: 4416663 INFO @ Sun, 21 Jun 2020 17:56:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:56:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 17:56:24: #1 tags after filtering in treatment: 4416642 INFO @ Sun, 21 Jun 2020 17:56:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:56:24: #1 finished! INFO @ Sun, 21 Jun 2020 17:56:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:56:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:56:24: #2 number of paired peaks: 393 WARNING @ Sun, 21 Jun 2020 17:56:24: Fewer paired peaks (393) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 393 pairs to build model! INFO @ Sun, 21 Jun 2020 17:56:24: start model_add_line... INFO @ Sun, 21 Jun 2020 17:56:24: start X-correlation... INFO @ Sun, 21 Jun 2020 17:56:24: end of X-cor INFO @ Sun, 21 Jun 2020 17:56:24: #2 finished! INFO @ Sun, 21 Jun 2020 17:56:24: #2 predicted fragment length is 59 bps INFO @ Sun, 21 Jun 2020 17:56:24: #2 alternative fragment length(s) may be 59 bps INFO @ Sun, 21 Jun 2020 17:56:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX124477/SRX124477.05_model.r WARNING @ Sun, 21 Jun 2020 17:56:24: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:56:24: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Sun, 21 Jun 2020 17:56:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 17:56:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:56:24: #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 @ Sun, 21 Jun 2020 17:56:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX124477/SRX124477.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX124477/SRX124477.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX124477/SRX124477.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX124477/SRX124477.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 @ Sun, 21 Jun 2020 17:56:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:56:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:56:32: 1000000 INFO @ Sun, 21 Jun 2020 17:56:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:56:37: 2000000 INFO @ Sun, 21 Jun 2020 17:56:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX124477/SRX124477.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:56:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX124477/SRX124477.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:56:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX124477/SRX124477.05_summits.bed INFO @ Sun, 21 Jun 2020 17:56:38: Done! pass1 - making usageList (211 chroms): 1 millis pass2 - checking and writing primary data (510 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:56:42: 3000000 INFO @ Sun, 21 Jun 2020 17:56:47: 4000000 INFO @ Sun, 21 Jun 2020 17:56:49: #1 tag size is determined as 30 bps INFO @ Sun, 21 Jun 2020 17:56:49: #1 tag size = 30 INFO @ Sun, 21 Jun 2020 17:56:49: #1 total tags in treatment: 4416663 INFO @ Sun, 21 Jun 2020 17:56:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:56:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 17:56:50: #1 tags after filtering in treatment: 4416642 INFO @ Sun, 21 Jun 2020 17:56:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:56:50: #1 finished! INFO @ Sun, 21 Jun 2020 17:56:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:56:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:56:50: #2 number of paired peaks: 393 WARNING @ Sun, 21 Jun 2020 17:56:50: Fewer paired peaks (393) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 393 pairs to build model! INFO @ Sun, 21 Jun 2020 17:56:50: start model_add_line... INFO @ Sun, 21 Jun 2020 17:56:50: start X-correlation... INFO @ Sun, 21 Jun 2020 17:56:50: end of X-cor INFO @ Sun, 21 Jun 2020 17:56:50: #2 finished! INFO @ Sun, 21 Jun 2020 17:56:50: #2 predicted fragment length is 59 bps INFO @ Sun, 21 Jun 2020 17:56:50: #2 alternative fragment length(s) may be 59 bps INFO @ Sun, 21 Jun 2020 17:56:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX124477/SRX124477.10_model.r WARNING @ Sun, 21 Jun 2020 17:56:50: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:56:50: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Sun, 21 Jun 2020 17:56:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 17:56:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:56:50: #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 @ Sun, 21 Jun 2020 17:56:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX124477/SRX124477.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX124477/SRX124477.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX124477/SRX124477.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX124477/SRX124477.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 @ Sun, 21 Jun 2020 17:56:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:56:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:56:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:57:02: 1000000 INFO @ Sun, 21 Jun 2020 17:57:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX124477/SRX124477.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:57:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX124477/SRX124477.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:57:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX124477/SRX124477.10_summits.bed INFO @ Sun, 21 Jun 2020 17:57:04: Done! pass1 - making usageList (114 chroms): 1 millis pass2 - checking and writing primary data (241 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:57:07: 2000000 INFO @ Sun, 21 Jun 2020 17:57:12: 3000000 INFO @ Sun, 21 Jun 2020 17:57:17: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:57:20: #1 tag size is determined as 30 bps INFO @ Sun, 21 Jun 2020 17:57:20: #1 tag size = 30 INFO @ Sun, 21 Jun 2020 17:57:20: #1 total tags in treatment: 4416663 INFO @ Sun, 21 Jun 2020 17:57:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:57:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 17:57:20: #1 tags after filtering in treatment: 4416642 INFO @ Sun, 21 Jun 2020 17:57:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:57:20: #1 finished! INFO @ Sun, 21 Jun 2020 17:57:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:57:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:57:20: #2 number of paired peaks: 393 WARNING @ Sun, 21 Jun 2020 17:57:20: Fewer paired peaks (393) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 393 pairs to build model! INFO @ Sun, 21 Jun 2020 17:57:20: start model_add_line... INFO @ Sun, 21 Jun 2020 17:57:20: start X-correlation... INFO @ Sun, 21 Jun 2020 17:57:20: end of X-cor INFO @ Sun, 21 Jun 2020 17:57:20: #2 finished! INFO @ Sun, 21 Jun 2020 17:57:20: #2 predicted fragment length is 59 bps INFO @ Sun, 21 Jun 2020 17:57:20: #2 alternative fragment length(s) may be 59 bps INFO @ Sun, 21 Jun 2020 17:57:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX124477/SRX124477.20_model.r WARNING @ Sun, 21 Jun 2020 17:57:20: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:57:20: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Sun, 21 Jun 2020 17:57:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 17:57:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:57:20: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:57:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:57:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX124477/SRX124477.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:57:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX124477/SRX124477.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:57:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX124477/SRX124477.20_summits.bed INFO @ Sun, 21 Jun 2020 17:57:35: Done! pass1 - making usageList (71 chroms): 0 millis pass2 - checking and writing primary data (119 records, 4 fields): 4 millis CompletedMACS2peakCalling