Job ID = 6452528 SRX = SRX016143 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:59:23 prefetch.2.10.7: 1) Downloading 'SRR034695'... 2020-06-21T07:59:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:01:39 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:01:39 prefetch.2.10.7: 'SRR034695' is valid 2020-06-21T08:01:39 prefetch.2.10.7: 1) 'SRR034695' was downloaded successfully Read 11863549 spots for SRR034695/SRR034695.sra Written 11863549 spots for SRR034695/SRR034695.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: 00:02:22 11863549 reads; of these: 11863549 (100.00%) were unpaired; of these: 761235 (6.42%) aligned 0 times 9043508 (76.23%) aligned exactly 1 time 2058806 (17.35%) aligned >1 times 93.58% overall alignment rate Time searching: 00:02:22 Overall time: 00:02:22 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] 1227768 / 11102314 = 0.1106 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 17:07:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX016143/SRX016143.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX016143/SRX016143.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX016143/SRX016143.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX016143/SRX016143.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 17:07:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:07:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:07:33: 1000000 INFO @ Sun, 21 Jun 2020 17:07:37: 2000000 INFO @ Sun, 21 Jun 2020 17:07:42: 3000000 INFO @ Sun, 21 Jun 2020 17:07:47: 4000000 INFO @ Sun, 21 Jun 2020 17:07:51: 5000000 INFO @ Sun, 21 Jun 2020 17:07:56: 6000000 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 17:07:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX016143/SRX016143.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX016143/SRX016143.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX016143/SRX016143.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX016143/SRX016143.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 17:07:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:07:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:08:01: 7000000 INFO @ Sun, 21 Jun 2020 17:08:03: 1000000 INFO @ Sun, 21 Jun 2020 17:08:06: 8000000 INFO @ Sun, 21 Jun 2020 17:08:08: 2000000 INFO @ Sun, 21 Jun 2020 17:08:11: 9000000 INFO @ Sun, 21 Jun 2020 17:08:13: 3000000 INFO @ Sun, 21 Jun 2020 17:08:16: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:08:16: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:08:16: #1 total tags in treatment: 9874546 INFO @ Sun, 21 Jun 2020 17:08:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:08:16: #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 17:08:16: #1 tags after filtering in treatment: 9874531 INFO @ Sun, 21 Jun 2020 17:08:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:08:16: #1 finished! INFO @ Sun, 21 Jun 2020 17:08:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:08:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:08:17: #2 number of paired peaks: 230 WARNING @ Sun, 21 Jun 2020 17:08:17: Fewer paired peaks (230) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 230 pairs to build model! INFO @ Sun, 21 Jun 2020 17:08:17: start model_add_line... INFO @ Sun, 21 Jun 2020 17:08:17: start X-correlation... INFO @ Sun, 21 Jun 2020 17:08:17: end of X-cor INFO @ Sun, 21 Jun 2020 17:08:17: #2 finished! INFO @ Sun, 21 Jun 2020 17:08:17: #2 predicted fragment length is 49 bps INFO @ Sun, 21 Jun 2020 17:08:17: #2 alternative fragment length(s) may be 4,49 bps INFO @ Sun, 21 Jun 2020 17:08:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX016143/SRX016143.05_model.r WARNING @ Sun, 21 Jun 2020 17:08:17: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:08:17: #2 You may need to consider one of the other alternative d(s): 4,49 WARNING @ Sun, 21 Jun 2020 17:08:17: #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 17:08:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:08:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:08:18: 4000000 INFO @ Sun, 21 Jun 2020 17:08:23: 5000000 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 17:08:28: 6000000 INFO @ Sun, 21 Jun 2020 17:08:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX016143/SRX016143.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX016143/SRX016143.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX016143/SRX016143.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX016143/SRX016143.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 17:08:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:08:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:08:33: 7000000 INFO @ Sun, 21 Jun 2020 17:08:33: 1000000 INFO @ Sun, 21 Jun 2020 17:08:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:08:38: 8000000 INFO @ Sun, 21 Jun 2020 17:08:38: 2000000 INFO @ Sun, 21 Jun 2020 17:08:43: 9000000 INFO @ Sun, 21 Jun 2020 17:08:43: 3000000 INFO @ Sun, 21 Jun 2020 17:08:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX016143/SRX016143.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:08:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX016143/SRX016143.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:08:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX016143/SRX016143.05_summits.bed INFO @ Sun, 21 Jun 2020 17:08:48: Done! INFO @ Sun, 21 Jun 2020 17:08:48: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:08:48: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:08:48: #1 total tags in treatment: 9874546 INFO @ Sun, 21 Jun 2020 17:08:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:08:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (233 chroms): 4 millis pass2 - checking and writing primary data (1449 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:08:48: #1 tags after filtering in treatment: 9874531 INFO @ Sun, 21 Jun 2020 17:08:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:08:48: #1 finished! INFO @ Sun, 21 Jun 2020 17:08:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:08:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:08:48: 4000000 INFO @ Sun, 21 Jun 2020 17:08:49: #2 number of paired peaks: 230 WARNING @ Sun, 21 Jun 2020 17:08:49: Fewer paired peaks (230) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 230 pairs to build model! INFO @ Sun, 21 Jun 2020 17:08:49: start model_add_line... INFO @ Sun, 21 Jun 2020 17:08:49: start X-correlation... INFO @ Sun, 21 Jun 2020 17:08:49: end of X-cor INFO @ Sun, 21 Jun 2020 17:08:49: #2 finished! INFO @ Sun, 21 Jun 2020 17:08:49: #2 predicted fragment length is 49 bps INFO @ Sun, 21 Jun 2020 17:08:49: #2 alternative fragment length(s) may be 4,49 bps INFO @ Sun, 21 Jun 2020 17:08:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX016143/SRX016143.10_model.r WARNING @ Sun, 21 Jun 2020 17:08:49: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:08:49: #2 You may need to consider one of the other alternative d(s): 4,49 WARNING @ Sun, 21 Jun 2020 17:08:49: #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 17:08:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:08:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:08:53: 5000000 INFO @ Sun, 21 Jun 2020 17:08:58: 6000000 INFO @ Sun, 21 Jun 2020 17:09:03: 7000000 INFO @ Sun, 21 Jun 2020 17:09:07: 8000000 INFO @ Sun, 21 Jun 2020 17:09:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:09:13: 9000000 INFO @ Sun, 21 Jun 2020 17:09:17: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:09:17: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:09:17: #1 total tags in treatment: 9874546 INFO @ Sun, 21 Jun 2020 17:09:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:09:17: #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 17:09:17: #1 tags after filtering in treatment: 9874531 INFO @ Sun, 21 Jun 2020 17:09:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:09:17: #1 finished! INFO @ Sun, 21 Jun 2020 17:09:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:09:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:09:18: #2 number of paired peaks: 230 WARNING @ Sun, 21 Jun 2020 17:09:18: Fewer paired peaks (230) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 230 pairs to build model! INFO @ Sun, 21 Jun 2020 17:09:18: start model_add_line... INFO @ Sun, 21 Jun 2020 17:09:18: start X-correlation... INFO @ Sun, 21 Jun 2020 17:09:18: end of X-cor INFO @ Sun, 21 Jun 2020 17:09:18: #2 finished! INFO @ Sun, 21 Jun 2020 17:09:18: #2 predicted fragment length is 49 bps INFO @ Sun, 21 Jun 2020 17:09:18: #2 alternative fragment length(s) may be 4,49 bps INFO @ Sun, 21 Jun 2020 17:09:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX016143/SRX016143.20_model.r WARNING @ Sun, 21 Jun 2020 17:09:18: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:09:18: #2 You may need to consider one of the other alternative d(s): 4,49 WARNING @ Sun, 21 Jun 2020 17:09:18: #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 17:09:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:09:18: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:09:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX016143/SRX016143.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:09:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX016143/SRX016143.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:09:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX016143/SRX016143.10_summits.bed INFO @ Sun, 21 Jun 2020 17:09:20: Done! pass1 - making usageList (112 chroms): 1 millis pass2 - checking and writing primary data (321 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:09:37: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:09:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX016143/SRX016143.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:09:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX016143/SRX016143.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:09:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX016143/SRX016143.20_summits.bed INFO @ Sun, 21 Jun 2020 17:09:48: Done! pass1 - making usageList (77 chroms): 1 millis pass2 - checking and writing primary data (145 records, 4 fields): 3 millis CompletedMACS2peakCalling