Job ID = 6456517 SRX = SRX359796 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:54:46 prefetch.2.10.7: 1) Downloading 'SRR1002328'... 2020-06-21T10:54:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:57:42 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:57:43 prefetch.2.10.7: 'SRR1002328' is valid 2020-06-21T10:57:43 prefetch.2.10.7: 1) 'SRR1002328' was downloaded successfully Read 14094683 spots for SRR1002328/SRR1002328.sra Written 14094683 spots for SRR1002328/SRR1002328.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: 00:03:29 14094683 reads; of these: 14094683 (100.00%) were unpaired; of these: 1243212 (8.82%) aligned 0 times 9324879 (66.16%) aligned exactly 1 time 3526592 (25.02%) aligned >1 times 91.18% overall alignment rate Time searching: 00:03:29 Overall time: 00:03:29 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_sort_core] merging from 8 files... [bam_rmdupse_core] 2201457 / 12851471 = 0.1713 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 20:06:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX359796/SRX359796.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX359796/SRX359796.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX359796/SRX359796.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX359796/SRX359796.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 20:06:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:06:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:06:23: 1000000 INFO @ Sun, 21 Jun 2020 20:06:28: 2000000 INFO @ Sun, 21 Jun 2020 20:06:33: 3000000 INFO @ Sun, 21 Jun 2020 20:06:38: 4000000 INFO @ Sun, 21 Jun 2020 20:06:43: 5000000 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 20:06:48: 6000000 INFO @ Sun, 21 Jun 2020 20:06:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX359796/SRX359796.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX359796/SRX359796.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX359796/SRX359796.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX359796/SRX359796.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 20:06:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:06:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:06:53: 7000000 INFO @ Sun, 21 Jun 2020 20:06:53: 1000000 INFO @ Sun, 21 Jun 2020 20:06:59: 8000000 INFO @ Sun, 21 Jun 2020 20:06:59: 2000000 INFO @ Sun, 21 Jun 2020 20:07:05: 9000000 INFO @ Sun, 21 Jun 2020 20:07:05: 3000000 INFO @ Sun, 21 Jun 2020 20:07:10: 10000000 INFO @ Sun, 21 Jun 2020 20:07:11: 4000000 INFO @ Sun, 21 Jun 2020 20:07:14: #1 tag size is determined as 46 bps INFO @ Sun, 21 Jun 2020 20:07:14: #1 tag size = 46 INFO @ Sun, 21 Jun 2020 20:07:14: #1 total tags in treatment: 10650014 INFO @ Sun, 21 Jun 2020 20:07:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:07:14: #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 20:07:15: #1 tags after filtering in treatment: 10649901 INFO @ Sun, 21 Jun 2020 20:07:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:07:15: #1 finished! INFO @ Sun, 21 Jun 2020 20:07:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:07:15: #2 looking for paired plus/minus strand peaks... 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 20:07:16: #2 number of paired peaks: 823 WARNING @ Sun, 21 Jun 2020 20:07:16: Fewer paired peaks (823) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 823 pairs to build model! INFO @ Sun, 21 Jun 2020 20:07:16: start model_add_line... INFO @ Sun, 21 Jun 2020 20:07:16: start X-correlation... INFO @ Sun, 21 Jun 2020 20:07:16: end of X-cor INFO @ Sun, 21 Jun 2020 20:07:16: #2 finished! INFO @ Sun, 21 Jun 2020 20:07:16: #2 predicted fragment length is 71 bps INFO @ Sun, 21 Jun 2020 20:07:16: #2 alternative fragment length(s) may be 4,71,590 bps INFO @ Sun, 21 Jun 2020 20:07:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX359796/SRX359796.05_model.r WARNING @ Sun, 21 Jun 2020 20:07:16: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:07:16: #2 You may need to consider one of the other alternative d(s): 4,71,590 WARNING @ Sun, 21 Jun 2020 20:07:16: #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 20:07:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:07:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:07:17: 5000000 INFO @ Sun, 21 Jun 2020 20:07:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX359796/SRX359796.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX359796/SRX359796.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX359796/SRX359796.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX359796/SRX359796.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 20:07:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:07:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:07:23: 6000000 INFO @ Sun, 21 Jun 2020 20:07:24: 1000000 INFO @ Sun, 21 Jun 2020 20:07:29: 7000000 INFO @ Sun, 21 Jun 2020 20:07:29: 2000000 INFO @ Sun, 21 Jun 2020 20:07:34: 8000000 INFO @ Sun, 21 Jun 2020 20:07:35: 3000000 INFO @ Sun, 21 Jun 2020 20:07:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:07:41: 4000000 INFO @ Sun, 21 Jun 2020 20:07:41: 9000000 INFO @ Sun, 21 Jun 2020 20:07:47: 5000000 INFO @ Sun, 21 Jun 2020 20:07:48: 10000000 INFO @ Sun, 21 Jun 2020 20:07:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX359796/SRX359796.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:07:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX359796/SRX359796.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:07:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX359796/SRX359796.05_summits.bed INFO @ Sun, 21 Jun 2020 20:07:48: Done! pass1 - making usageList (528 chroms): 1 millis pass2 - checking and writing primary data (2084 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:07:52: #1 tag size is determined as 46 bps INFO @ Sun, 21 Jun 2020 20:07:52: #1 tag size = 46 INFO @ Sun, 21 Jun 2020 20:07:52: #1 total tags in treatment: 10650014 INFO @ Sun, 21 Jun 2020 20:07:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:07:52: #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 20:07:53: #1 tags after filtering in treatment: 10649901 INFO @ Sun, 21 Jun 2020 20:07:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:07:53: #1 finished! INFO @ Sun, 21 Jun 2020 20:07:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:07:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:07:54: 6000000 INFO @ Sun, 21 Jun 2020 20:07:54: #2 number of paired peaks: 823 WARNING @ Sun, 21 Jun 2020 20:07:54: Fewer paired peaks (823) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 823 pairs to build model! INFO @ Sun, 21 Jun 2020 20:07:54: start model_add_line... INFO @ Sun, 21 Jun 2020 20:07:54: start X-correlation... INFO @ Sun, 21 Jun 2020 20:07:54: end of X-cor INFO @ Sun, 21 Jun 2020 20:07:54: #2 finished! INFO @ Sun, 21 Jun 2020 20:07:54: #2 predicted fragment length is 71 bps INFO @ Sun, 21 Jun 2020 20:07:54: #2 alternative fragment length(s) may be 4,71,590 bps INFO @ Sun, 21 Jun 2020 20:07:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX359796/SRX359796.10_model.r WARNING @ Sun, 21 Jun 2020 20:07:54: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:07:54: #2 You may need to consider one of the other alternative d(s): 4,71,590 WARNING @ Sun, 21 Jun 2020 20:07:54: #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 20:07:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:07:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:08:00: 7000000 INFO @ Sun, 21 Jun 2020 20:08:06: 8000000 INFO @ Sun, 21 Jun 2020 20:08:13: 9000000 INFO @ Sun, 21 Jun 2020 20:08:15: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:08:20: 10000000 INFO @ Sun, 21 Jun 2020 20:08:24: #1 tag size is determined as 46 bps INFO @ Sun, 21 Jun 2020 20:08:24: #1 tag size = 46 INFO @ Sun, 21 Jun 2020 20:08:24: #1 total tags in treatment: 10650014 INFO @ Sun, 21 Jun 2020 20:08:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:08:24: #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 20:08:25: #1 tags after filtering in treatment: 10649901 INFO @ Sun, 21 Jun 2020 20:08:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:08:25: #1 finished! INFO @ Sun, 21 Jun 2020 20:08:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:08:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:08:26: #2 number of paired peaks: 823 WARNING @ Sun, 21 Jun 2020 20:08:26: Fewer paired peaks (823) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 823 pairs to build model! INFO @ Sun, 21 Jun 2020 20:08:26: start model_add_line... INFO @ Sun, 21 Jun 2020 20:08:26: start X-correlation... INFO @ Sun, 21 Jun 2020 20:08:26: end of X-cor INFO @ Sun, 21 Jun 2020 20:08:26: #2 finished! INFO @ Sun, 21 Jun 2020 20:08:26: #2 predicted fragment length is 71 bps INFO @ Sun, 21 Jun 2020 20:08:26: #2 alternative fragment length(s) may be 4,71,590 bps INFO @ Sun, 21 Jun 2020 20:08:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX359796/SRX359796.20_model.r WARNING @ Sun, 21 Jun 2020 20:08:26: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:08:26: #2 You may need to consider one of the other alternative d(s): 4,71,590 WARNING @ Sun, 21 Jun 2020 20:08:26: #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 20:08:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:08:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:08:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX359796/SRX359796.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:08:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX359796/SRX359796.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:08:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX359796/SRX359796.10_summits.bed INFO @ Sun, 21 Jun 2020 20:08:26: Done! pass1 - making usageList (292 chroms): 2 millis pass2 - checking and writing primary data (809 records, 4 fields): 17 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:08:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:08:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX359796/SRX359796.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:08:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX359796/SRX359796.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:08:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX359796/SRX359796.20_summits.bed INFO @ Sun, 21 Jun 2020 20:08:58: Done! pass1 - making usageList (130 chroms): 1 millis pass2 - checking and writing primary data (297 records, 4 fields): 8 millis CompletedMACS2peakCalling