Job ID = 6529478 SRX = SRX287746 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:06:57 21494133 reads; of these: 21494133 (100.00%) were unpaired; of these: 1544664 (7.19%) aligned 0 times 13572991 (63.15%) aligned exactly 1 time 6376478 (29.67%) aligned >1 times 92.81% overall alignment rate Time searching: 00:06:57 Overall time: 00:06:57 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 12 files... [bam_rmdupse_core] 3736518 / 19949469 = 0.1873 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 @ Tue, 30 Jun 2020 02:29:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287746/SRX287746.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287746/SRX287746.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287746/SRX287746.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287746/SRX287746.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 @ Tue, 30 Jun 2020 02:29:20: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:29:20: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:29:26: 1000000 INFO @ Tue, 30 Jun 2020 02:29:31: 2000000 INFO @ Tue, 30 Jun 2020 02:29:37: 3000000 INFO @ Tue, 30 Jun 2020 02:29:43: 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 @ Tue, 30 Jun 2020 02:29:49: 5000000 INFO @ Tue, 30 Jun 2020 02:29:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287746/SRX287746.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287746/SRX287746.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287746/SRX287746.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287746/SRX287746.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 @ Tue, 30 Jun 2020 02:29:49: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:29:49: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:29:55: 6000000 INFO @ Tue, 30 Jun 2020 02:29:55: 1000000 INFO @ Tue, 30 Jun 2020 02:30:01: 7000000 INFO @ Tue, 30 Jun 2020 02:30:01: 2000000 INFO @ Tue, 30 Jun 2020 02:30:07: 8000000 INFO @ Tue, 30 Jun 2020 02:30:07: 3000000 INFO @ Tue, 30 Jun 2020 02:30:13: 9000000 INFO @ Tue, 30 Jun 2020 02:30:13: 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 @ Tue, 30 Jun 2020 02:30:18: 10000000 INFO @ Tue, 30 Jun 2020 02:30:19: 5000000 INFO @ Tue, 30 Jun 2020 02:30:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287746/SRX287746.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287746/SRX287746.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287746/SRX287746.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287746/SRX287746.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 @ Tue, 30 Jun 2020 02:30:19: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:30:19: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:30:25: 11000000 INFO @ Tue, 30 Jun 2020 02:30:25: 6000000 INFO @ Tue, 30 Jun 2020 02:30:26: 1000000 INFO @ Tue, 30 Jun 2020 02:30:31: 12000000 INFO @ Tue, 30 Jun 2020 02:30:31: 7000000 INFO @ Tue, 30 Jun 2020 02:30:32: 2000000 INFO @ Tue, 30 Jun 2020 02:30:37: 8000000 INFO @ Tue, 30 Jun 2020 02:30:37: 13000000 INFO @ Tue, 30 Jun 2020 02:30:38: 3000000 INFO @ Tue, 30 Jun 2020 02:30:43: 9000000 INFO @ Tue, 30 Jun 2020 02:30:43: 14000000 INFO @ Tue, 30 Jun 2020 02:30:45: 4000000 INFO @ Tue, 30 Jun 2020 02:30:48: 10000000 INFO @ Tue, 30 Jun 2020 02:30:49: 15000000 INFO @ Tue, 30 Jun 2020 02:30:51: 5000000 INFO @ Tue, 30 Jun 2020 02:30:54: 11000000 INFO @ Tue, 30 Jun 2020 02:30:56: 16000000 INFO @ Tue, 30 Jun 2020 02:30:57: 6000000 INFO @ Tue, 30 Jun 2020 02:30:58: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:30:58: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:30:58: #1 total tags in treatment: 16212951 INFO @ Tue, 30 Jun 2020 02:30:58: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:30:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:30:58: #1 tags after filtering in treatment: 16212951 INFO @ Tue, 30 Jun 2020 02:30:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:30:58: #1 finished! INFO @ Tue, 30 Jun 2020 02:30:58: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:30:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:31:00: #2 number of paired peaks: 754 WARNING @ Tue, 30 Jun 2020 02:31:00: Fewer paired peaks (754) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 754 pairs to build model! INFO @ Tue, 30 Jun 2020 02:31:00: start model_add_line... INFO @ Tue, 30 Jun 2020 02:31:00: start X-correlation... INFO @ Tue, 30 Jun 2020 02:31:00: end of X-cor INFO @ Tue, 30 Jun 2020 02:31:00: #2 finished! INFO @ Tue, 30 Jun 2020 02:31:00: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:31:00: #2 alternative fragment length(s) may be 2,18,31,572 bps INFO @ Tue, 30 Jun 2020 02:31:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287746/SRX287746.05_model.r WARNING @ Tue, 30 Jun 2020 02:31:00: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:31:00: #2 You may need to consider one of the other alternative d(s): 2,18,31,572 WARNING @ Tue, 30 Jun 2020 02:31:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:31:00: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:31:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:31:00: 12000000 INFO @ Tue, 30 Jun 2020 02:31:03: 7000000 INFO @ Tue, 30 Jun 2020 02:31:07: 13000000 INFO @ Tue, 30 Jun 2020 02:31:09: 8000000 INFO @ Tue, 30 Jun 2020 02:31:12: 14000000 INFO @ Tue, 30 Jun 2020 02:31:14: 9000000 INFO @ Tue, 30 Jun 2020 02:31:18: 15000000 INFO @ Tue, 30 Jun 2020 02:31:20: 10000000 INFO @ Tue, 30 Jun 2020 02:31:24: 16000000 INFO @ Tue, 30 Jun 2020 02:31:26: 11000000 INFO @ Tue, 30 Jun 2020 02:31:26: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:31:26: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:31:26: #1 total tags in treatment: 16212951 INFO @ Tue, 30 Jun 2020 02:31:26: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:31:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:31:26: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:31:27: #1 tags after filtering in treatment: 16212951 INFO @ Tue, 30 Jun 2020 02:31:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:31:27: #1 finished! INFO @ Tue, 30 Jun 2020 02:31:27: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:31:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:31:28: #2 number of paired peaks: 754 WARNING @ Tue, 30 Jun 2020 02:31:28: Fewer paired peaks (754) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 754 pairs to build model! INFO @ Tue, 30 Jun 2020 02:31:28: start model_add_line... INFO @ Tue, 30 Jun 2020 02:31:28: start X-correlation... INFO @ Tue, 30 Jun 2020 02:31:28: end of X-cor INFO @ Tue, 30 Jun 2020 02:31:28: #2 finished! INFO @ Tue, 30 Jun 2020 02:31:28: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:31:28: #2 alternative fragment length(s) may be 2,18,31,572 bps INFO @ Tue, 30 Jun 2020 02:31:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287746/SRX287746.10_model.r WARNING @ Tue, 30 Jun 2020 02:31:28: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:31:28: #2 You may need to consider one of the other alternative d(s): 2,18,31,572 WARNING @ Tue, 30 Jun 2020 02:31:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:31:28: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:31:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:31:31: 12000000 INFO @ Tue, 30 Jun 2020 02:31:38: 13000000 INFO @ Tue, 30 Jun 2020 02:31:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287746/SRX287746.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:31:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287746/SRX287746.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:31:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287746/SRX287746.05_summits.bed INFO @ Tue, 30 Jun 2020 02:31:40: Done! pass1 - making usageList (0 chroms): 4 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:31:44: 14000000 INFO @ Tue, 30 Jun 2020 02:31:49: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:31:55: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:31:55: 16000000 INFO @ Tue, 30 Jun 2020 02:31:57: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:31:57: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:31:57: #1 total tags in treatment: 16212951 INFO @ Tue, 30 Jun 2020 02:31:57: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:31:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:31:58: #1 tags after filtering in treatment: 16212951 INFO @ Tue, 30 Jun 2020 02:31:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:31:58: #1 finished! INFO @ Tue, 30 Jun 2020 02:31:58: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:31:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:31:59: #2 number of paired peaks: 754 WARNING @ Tue, 30 Jun 2020 02:31:59: Fewer paired peaks (754) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 754 pairs to build model! INFO @ Tue, 30 Jun 2020 02:31:59: start model_add_line... INFO @ Tue, 30 Jun 2020 02:31:59: start X-correlation... INFO @ Tue, 30 Jun 2020 02:31:59: end of X-cor INFO @ Tue, 30 Jun 2020 02:31:59: #2 finished! INFO @ Tue, 30 Jun 2020 02:31:59: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:31:59: #2 alternative fragment length(s) may be 2,18,31,572 bps INFO @ Tue, 30 Jun 2020 02:31:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287746/SRX287746.20_model.r WARNING @ Tue, 30 Jun 2020 02:31:59: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:31:59: #2 You may need to consider one of the other alternative d(s): 2,18,31,572 WARNING @ Tue, 30 Jun 2020 02:31:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:31:59: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:31:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:32:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287746/SRX287746.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:32:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287746/SRX287746.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:32:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287746/SRX287746.10_summits.bed INFO @ Tue, 30 Jun 2020 02:32:08: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:32:26: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:32:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287746/SRX287746.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:32:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287746/SRX287746.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:32:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287746/SRX287746.20_summits.bed INFO @ Tue, 30 Jun 2020 02:32:39: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling