Job ID = 6529453 SRX = SRX287590 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: 00:05:55 19172821 reads; of these: 19172821 (100.00%) were unpaired; of these: 908436 (4.74%) aligned 0 times 12595482 (65.69%) aligned exactly 1 time 5668903 (29.57%) aligned >1 times 95.26% overall alignment rate Time searching: 00:05:55 Overall time: 00:05:55 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] 3545027 / 18264385 = 0.1941 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 02:13:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287590/SRX287590.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287590/SRX287590.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287590/SRX287590.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287590/SRX287590.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 02:13:20: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:13:20: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:13:27: 1000000 INFO @ Tue, 30 Jun 2020 02:13:35: 2000000 INFO @ Tue, 30 Jun 2020 02:13:43: 3000000 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 02:13:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287590/SRX287590.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287590/SRX287590.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287590/SRX287590.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287590/SRX287590.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 02:13:50: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:13:50: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:13:51: 4000000 INFO @ Tue, 30 Jun 2020 02:13:58: 1000000 INFO @ Tue, 30 Jun 2020 02:13:59: 5000000 INFO @ Tue, 30 Jun 2020 02:14:06: 2000000 INFO @ Tue, 30 Jun 2020 02:14:07: 6000000 INFO @ Tue, 30 Jun 2020 02:14:14: 3000000 INFO @ Tue, 30 Jun 2020 02:14:15: 7000000 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 02:14:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287590/SRX287590.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287590/SRX287590.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287590/SRX287590.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287590/SRX287590.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 02:14:20: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:14:20: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:14:23: 8000000 INFO @ Tue, 30 Jun 2020 02:14:23: 4000000 INFO @ Tue, 30 Jun 2020 02:14:26: 1000000 INFO @ Tue, 30 Jun 2020 02:14:30: 9000000 INFO @ Tue, 30 Jun 2020 02:14:31: 5000000 INFO @ Tue, 30 Jun 2020 02:14:33: 2000000 INFO @ Tue, 30 Jun 2020 02:14:38: 10000000 INFO @ Tue, 30 Jun 2020 02:14:38: 6000000 INFO @ Tue, 30 Jun 2020 02:14:40: 3000000 INFO @ Tue, 30 Jun 2020 02:14:46: 11000000 INFO @ Tue, 30 Jun 2020 02:14:46: 7000000 INFO @ Tue, 30 Jun 2020 02:14:47: 4000000 INFO @ Tue, 30 Jun 2020 02:14:54: 8000000 INFO @ Tue, 30 Jun 2020 02:14:55: 12000000 INFO @ Tue, 30 Jun 2020 02:14:55: 5000000 INFO @ Tue, 30 Jun 2020 02:15:02: 9000000 INFO @ Tue, 30 Jun 2020 02:15:02: 6000000 INFO @ Tue, 30 Jun 2020 02:15:02: 13000000 INFO @ Tue, 30 Jun 2020 02:15:09: 7000000 INFO @ Tue, 30 Jun 2020 02:15:09: 10000000 INFO @ Tue, 30 Jun 2020 02:15:10: 14000000 INFO @ Tue, 30 Jun 2020 02:15:16: 8000000 INFO @ Tue, 30 Jun 2020 02:15:16: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:15:16: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:15:16: #1 total tags in treatment: 14719358 INFO @ Tue, 30 Jun 2020 02:15:16: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:15:16: #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 02:15:17: #1 tags after filtering in treatment: 14719358 INFO @ Tue, 30 Jun 2020 02:15:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:15:17: #1 finished! INFO @ Tue, 30 Jun 2020 02:15:17: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:15:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:15:17: 11000000 INFO @ Tue, 30 Jun 2020 02:15:18: #2 number of paired peaks: 674 WARNING @ Tue, 30 Jun 2020 02:15:18: Fewer paired peaks (674) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 674 pairs to build model! INFO @ Tue, 30 Jun 2020 02:15:18: start model_add_line... INFO @ Tue, 30 Jun 2020 02:15:18: start X-correlation... INFO @ Tue, 30 Jun 2020 02:15:18: end of X-cor INFO @ Tue, 30 Jun 2020 02:15:18: #2 finished! INFO @ Tue, 30 Jun 2020 02:15:18: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:15:18: #2 alternative fragment length(s) may be 2,29 bps INFO @ Tue, 30 Jun 2020 02:15:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287590/SRX287590.05_model.r WARNING @ Tue, 30 Jun 2020 02:15:18: #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 02:15:18: #2 You may need to consider one of the other alternative d(s): 2,29 WARNING @ Tue, 30 Jun 2020 02:15:18: #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 02:15:18: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:15:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:15:23: 9000000 INFO @ Tue, 30 Jun 2020 02:15:25: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:15:29: 10000000 INFO @ Tue, 30 Jun 2020 02:15:32: 13000000 INFO @ Tue, 30 Jun 2020 02:15:36: 11000000 INFO @ Tue, 30 Jun 2020 02:15:40: 14000000 INFO @ Tue, 30 Jun 2020 02:15:44: 12000000 INFO @ Tue, 30 Jun 2020 02:15:44: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:15:45: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:15:45: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:15:45: #1 total tags in treatment: 14719358 INFO @ Tue, 30 Jun 2020 02:15:45: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:15:45: #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 02:15:46: #1 tags after filtering in treatment: 14719358 INFO @ Tue, 30 Jun 2020 02:15:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:15:46: #1 finished! INFO @ Tue, 30 Jun 2020 02:15:46: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:15:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:15:47: #2 number of paired peaks: 674 WARNING @ Tue, 30 Jun 2020 02:15:47: Fewer paired peaks (674) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 674 pairs to build model! INFO @ Tue, 30 Jun 2020 02:15:47: start model_add_line... INFO @ Tue, 30 Jun 2020 02:15:47: start X-correlation... INFO @ Tue, 30 Jun 2020 02:15:47: end of X-cor INFO @ Tue, 30 Jun 2020 02:15:47: #2 finished! INFO @ Tue, 30 Jun 2020 02:15:47: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:15:47: #2 alternative fragment length(s) may be 2,29 bps INFO @ Tue, 30 Jun 2020 02:15:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287590/SRX287590.10_model.r WARNING @ Tue, 30 Jun 2020 02:15:47: #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 02:15:47: #2 You may need to consider one of the other alternative d(s): 2,29 WARNING @ Tue, 30 Jun 2020 02:15:47: #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 02:15:47: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:15:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:15:50: 13000000 INFO @ Tue, 30 Jun 2020 02:15:56: 14000000 INFO @ Tue, 30 Jun 2020 02:15:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287590/SRX287590.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:15:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287590/SRX287590.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:15:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287590/SRX287590.05_summits.bed INFO @ Tue, 30 Jun 2020 02:15:56: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:16:01: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:16:01: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:16:01: #1 total tags in treatment: 14719358 INFO @ Tue, 30 Jun 2020 02:16:01: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:16:01: #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 02:16:02: #1 tags after filtering in treatment: 14719358 INFO @ Tue, 30 Jun 2020 02:16:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:16:02: #1 finished! INFO @ Tue, 30 Jun 2020 02:16:02: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:16:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:16:03: #2 number of paired peaks: 674 WARNING @ Tue, 30 Jun 2020 02:16:03: Fewer paired peaks (674) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 674 pairs to build model! INFO @ Tue, 30 Jun 2020 02:16:03: start model_add_line... INFO @ Tue, 30 Jun 2020 02:16:03: start X-correlation... INFO @ Tue, 30 Jun 2020 02:16:03: end of X-cor INFO @ Tue, 30 Jun 2020 02:16:03: #2 finished! INFO @ Tue, 30 Jun 2020 02:16:03: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:16:03: #2 alternative fragment length(s) may be 2,29 bps INFO @ Tue, 30 Jun 2020 02:16:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287590/SRX287590.20_model.r WARNING @ Tue, 30 Jun 2020 02:16:03: #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 02:16:03: #2 You may need to consider one of the other alternative d(s): 2,29 WARNING @ Tue, 30 Jun 2020 02:16:03: #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 02:16:03: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:16:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:16:13: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:16:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287590/SRX287590.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:16:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287590/SRX287590.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:16:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287590/SRX287590.10_summits.bed INFO @ Tue, 30 Jun 2020 02:16:26: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:16:30: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:16:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287590/SRX287590.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:16:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287590/SRX287590.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:16:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287590/SRX287590.20_summits.bed INFO @ Tue, 30 Jun 2020 02:16:43: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling