Job ID = 6498438 SRX = SRX495295 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T23:29:32 prefetch.2.10.7: 1) Downloading 'SRR1198800'... 2020-06-25T23:29:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:32:05 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:32:05 prefetch.2.10.7: 1) 'SRR1198800' was downloaded successfully Read 17643933 spots for SRR1198800/SRR1198800.sra Written 17643933 spots for SRR1198800/SRR1198800.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: 00:00:01 Multiseed full-index search: 00:06:51 17643933 reads; of these: 17643933 (100.00%) were unpaired; of these: 997754 (5.65%) aligned 0 times 11037573 (62.56%) aligned exactly 1 time 5608606 (31.79%) aligned >1 times 94.35% overall alignment rate Time searching: 00:06:52 Overall time: 00:06:52 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_sort_core] merging from 8 files... [bam_rmdupse_core] 3432432 / 16646179 = 0.2062 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 @ Fri, 26 Jun 2020 08:43:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495295/SRX495295.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495295/SRX495295.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495295/SRX495295.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495295/SRX495295.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 @ Fri, 26 Jun 2020 08:43:52: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:43:52: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:43:58: 1000000 INFO @ Fri, 26 Jun 2020 08:44:03: 2000000 INFO @ Fri, 26 Jun 2020 08:44:09: 3000000 INFO @ Fri, 26 Jun 2020 08:44:14: 4000000 INFO @ Fri, 26 Jun 2020 08:44:19: 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 @ Fri, 26 Jun 2020 08:44:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495295/SRX495295.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495295/SRX495295.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495295/SRX495295.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495295/SRX495295.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 @ Fri, 26 Jun 2020 08:44:22: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:44:22: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:44:25: 6000000 INFO @ Fri, 26 Jun 2020 08:44:28: 1000000 INFO @ Fri, 26 Jun 2020 08:44:30: 7000000 INFO @ Fri, 26 Jun 2020 08:44:34: 2000000 INFO @ Fri, 26 Jun 2020 08:44:36: 8000000 INFO @ Fri, 26 Jun 2020 08:44:39: 3000000 INFO @ Fri, 26 Jun 2020 08:44:42: 9000000 INFO @ Fri, 26 Jun 2020 08:44:45: 4000000 INFO @ Fri, 26 Jun 2020 08:44:48: 10000000 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 @ Fri, 26 Jun 2020 08:44:51: 5000000 INFO @ Fri, 26 Jun 2020 08:44:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495295/SRX495295.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495295/SRX495295.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495295/SRX495295.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495295/SRX495295.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 @ Fri, 26 Jun 2020 08:44:52: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:44:52: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:44:53: 11000000 INFO @ Fri, 26 Jun 2020 08:44:56: 6000000 INFO @ Fri, 26 Jun 2020 08:44:58: 1000000 INFO @ Fri, 26 Jun 2020 08:44:59: 12000000 INFO @ Fri, 26 Jun 2020 08:45:02: 7000000 INFO @ Fri, 26 Jun 2020 08:45:04: 2000000 INFO @ Fri, 26 Jun 2020 08:45:05: 13000000 INFO @ Fri, 26 Jun 2020 08:45:06: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:45:06: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:45:06: #1 total tags in treatment: 13213747 INFO @ Fri, 26 Jun 2020 08:45:06: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:45:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:45:06: #1 tags after filtering in treatment: 13213747 INFO @ Fri, 26 Jun 2020 08:45:06: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:45:06: #1 finished! INFO @ Fri, 26 Jun 2020 08:45:06: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:45:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:45:07: #2 number of paired peaks: 140 WARNING @ Fri, 26 Jun 2020 08:45:07: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Fri, 26 Jun 2020 08:45:07: start model_add_line... INFO @ Fri, 26 Jun 2020 08:45:07: start X-correlation... INFO @ Fri, 26 Jun 2020 08:45:07: end of X-cor INFO @ Fri, 26 Jun 2020 08:45:07: #2 finished! INFO @ Fri, 26 Jun 2020 08:45:07: #2 predicted fragment length is 47 bps INFO @ Fri, 26 Jun 2020 08:45:07: #2 alternative fragment length(s) may be 4,47 bps INFO @ Fri, 26 Jun 2020 08:45:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495295/SRX495295.05_model.r WARNING @ Fri, 26 Jun 2020 08:45:07: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:45:07: #2 You may need to consider one of the other alternative d(s): 4,47 WARNING @ Fri, 26 Jun 2020 08:45:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 08:45:07: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:45:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:45:08: 8000000 INFO @ Fri, 26 Jun 2020 08:45:10: 3000000 INFO @ Fri, 26 Jun 2020 08:45:14: 9000000 INFO @ Fri, 26 Jun 2020 08:45:15: 4000000 INFO @ Fri, 26 Jun 2020 08:45:20: 10000000 INFO @ Fri, 26 Jun 2020 08:45:21: 5000000 INFO @ Fri, 26 Jun 2020 08:45:25: 11000000 INFO @ Fri, 26 Jun 2020 08:45:27: 6000000 INFO @ Fri, 26 Jun 2020 08:45:31: 12000000 INFO @ Fri, 26 Jun 2020 08:45:33: 7000000 INFO @ Fri, 26 Jun 2020 08:45:36: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:45:37: 13000000 INFO @ Fri, 26 Jun 2020 08:45:38: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:45:38: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:45:38: #1 total tags in treatment: 13213747 INFO @ Fri, 26 Jun 2020 08:45:38: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:45:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:45:38: #1 tags after filtering in treatment: 13213747 INFO @ Fri, 26 Jun 2020 08:45:38: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:45:38: #1 finished! INFO @ Fri, 26 Jun 2020 08:45:38: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:45:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:45:39: 8000000 INFO @ Fri, 26 Jun 2020 08:45:39: #2 number of paired peaks: 140 WARNING @ Fri, 26 Jun 2020 08:45:39: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Fri, 26 Jun 2020 08:45:39: start model_add_line... INFO @ Fri, 26 Jun 2020 08:45:39: start X-correlation... INFO @ Fri, 26 Jun 2020 08:45:39: end of X-cor INFO @ Fri, 26 Jun 2020 08:45:39: #2 finished! INFO @ Fri, 26 Jun 2020 08:45:39: #2 predicted fragment length is 47 bps INFO @ Fri, 26 Jun 2020 08:45:39: #2 alternative fragment length(s) may be 4,47 bps INFO @ Fri, 26 Jun 2020 08:45:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495295/SRX495295.10_model.r WARNING @ Fri, 26 Jun 2020 08:45:39: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:45:39: #2 You may need to consider one of the other alternative d(s): 4,47 WARNING @ Fri, 26 Jun 2020 08:45:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 08:45:39: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:45:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:45:44: 9000000 INFO @ Fri, 26 Jun 2020 08:45:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495295/SRX495295.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:45:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495295/SRX495295.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:45:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495295/SRX495295.05_summits.bed INFO @ Fri, 26 Jun 2020 08:45:50: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1284 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:45:50: 10000000 INFO @ Fri, 26 Jun 2020 08:45:56: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:46:02: 12000000 INFO @ Fri, 26 Jun 2020 08:46:07: 13000000 INFO @ Fri, 26 Jun 2020 08:46:08: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:46:09: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:46:09: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:46:09: #1 total tags in treatment: 13213747 INFO @ Fri, 26 Jun 2020 08:46:09: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:46:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:46:09: #1 tags after filtering in treatment: 13213747 INFO @ Fri, 26 Jun 2020 08:46:09: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:46:09: #1 finished! INFO @ Fri, 26 Jun 2020 08:46:09: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:46:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:46:10: #2 number of paired peaks: 140 WARNING @ Fri, 26 Jun 2020 08:46:10: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Fri, 26 Jun 2020 08:46:10: start model_add_line... INFO @ Fri, 26 Jun 2020 08:46:10: start X-correlation... INFO @ Fri, 26 Jun 2020 08:46:10: end of X-cor INFO @ Fri, 26 Jun 2020 08:46:10: #2 finished! INFO @ Fri, 26 Jun 2020 08:46:10: #2 predicted fragment length is 47 bps INFO @ Fri, 26 Jun 2020 08:46:10: #2 alternative fragment length(s) may be 4,47 bps INFO @ Fri, 26 Jun 2020 08:46:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495295/SRX495295.20_model.r WARNING @ Fri, 26 Jun 2020 08:46:10: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:46:10: #2 You may need to consider one of the other alternative d(s): 4,47 WARNING @ Fri, 26 Jun 2020 08:46:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 08:46:10: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:46:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:46:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495295/SRX495295.10_peaks.xls INFO @ Fri, 26 Jun 2020 08:46:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495295/SRX495295.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:46:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495295/SRX495295.10_summits.bed INFO @ Fri, 26 Jun 2020 08:46:22: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (950 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 08:46:39: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:46:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495295/SRX495295.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:46:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495295/SRX495295.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:46:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495295/SRX495295.20_summits.bed INFO @ Fri, 26 Jun 2020 08:46:53: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (429 records, 4 fields): 2 millis CompletedMACS2peakCalling