Job ID = 6529784 SRX = SRX481091 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: 00:06:22 19172821 reads; of these: 19172821 (100.00%) were unpaired; of these: 908410 (4.74%) aligned 0 times 12595466 (65.69%) aligned exactly 1 time 5668945 (29.57%) aligned >1 times 95.26% overall alignment rate Time searching: 00:06:22 Overall time: 00:06:22 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_sort_core] merging from 8 files... [bam_rmdupse_core] 3545908 / 18264411 = 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 02:52:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX481091/SRX481091.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX481091/SRX481091.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX481091/SRX481091.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX481091/SRX481091.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 02:52:19: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:52:19: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:52:25: 1000000 INFO @ Tue, 30 Jun 2020 02:52:32: 2000000 INFO @ Tue, 30 Jun 2020 02:52:38: 3000000 INFO @ Tue, 30 Jun 2020 02:52:44: 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 02:52:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX481091/SRX481091.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX481091/SRX481091.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX481091/SRX481091.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX481091/SRX481091.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 02:52:49: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:52:49: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:52:51: 5000000 INFO @ Tue, 30 Jun 2020 02:52:56: 1000000 INFO @ Tue, 30 Jun 2020 02:52:58: 6000000 INFO @ Tue, 30 Jun 2020 02:53:03: 2000000 INFO @ Tue, 30 Jun 2020 02:53:05: 7000000 INFO @ Tue, 30 Jun 2020 02:53:10: 3000000 INFO @ Tue, 30 Jun 2020 02:53:12: 8000000 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 02:53:17: 4000000 INFO @ Tue, 30 Jun 2020 02:53:19: 9000000 INFO @ Tue, 30 Jun 2020 02:53:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX481091/SRX481091.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX481091/SRX481091.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX481091/SRX481091.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX481091/SRX481091.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 02:53:22: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:53:22: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:53:25: 5000000 INFO @ Tue, 30 Jun 2020 02:53:26: 10000000 INFO @ Tue, 30 Jun 2020 02:53:31: 1000000 INFO @ Tue, 30 Jun 2020 02:53:32: 6000000 INFO @ Tue, 30 Jun 2020 02:53:34: 11000000 INFO @ Tue, 30 Jun 2020 02:53:40: 2000000 INFO @ Tue, 30 Jun 2020 02:53:40: 7000000 INFO @ Tue, 30 Jun 2020 02:53:43: 12000000 INFO @ Tue, 30 Jun 2020 02:53:48: 8000000 INFO @ Tue, 30 Jun 2020 02:53:49: 3000000 INFO @ Tue, 30 Jun 2020 02:53:52: 13000000 INFO @ Tue, 30 Jun 2020 02:53:55: 9000000 INFO @ Tue, 30 Jun 2020 02:53:57: 4000000 INFO @ Tue, 30 Jun 2020 02:54:00: 14000000 INFO @ Tue, 30 Jun 2020 02:54:03: 10000000 INFO @ Tue, 30 Jun 2020 02:54:06: 5000000 INFO @ Tue, 30 Jun 2020 02:54:06: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:54:06: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:54:06: #1 total tags in treatment: 14718503 INFO @ Tue, 30 Jun 2020 02:54:06: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:54:06: #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 02:54:07: #1 tags after filtering in treatment: 14718503 INFO @ Tue, 30 Jun 2020 02:54:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:54:07: #1 finished! INFO @ Tue, 30 Jun 2020 02:54:07: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:54:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:54:08: #2 number of paired peaks: 691 WARNING @ Tue, 30 Jun 2020 02:54:08: Fewer paired peaks (691) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 691 pairs to build model! INFO @ Tue, 30 Jun 2020 02:54:08: start model_add_line... INFO @ Tue, 30 Jun 2020 02:54:08: start X-correlation... INFO @ Tue, 30 Jun 2020 02:54:08: end of X-cor INFO @ Tue, 30 Jun 2020 02:54:08: #2 finished! INFO @ Tue, 30 Jun 2020 02:54:08: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:54:08: #2 alternative fragment length(s) may be 2,24 bps INFO @ Tue, 30 Jun 2020 02:54:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX481091/SRX481091.05_model.r WARNING @ Tue, 30 Jun 2020 02:54:08: #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 02:54:08: #2 You may need to consider one of the other alternative d(s): 2,24 WARNING @ Tue, 30 Jun 2020 02:54:08: #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 02:54:08: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:54:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:54:10: 11000000 INFO @ Tue, 30 Jun 2020 02:54:15: 6000000 INFO @ Tue, 30 Jun 2020 02:54:18: 12000000 INFO @ Tue, 30 Jun 2020 02:54:23: 7000000 INFO @ Tue, 30 Jun 2020 02:54:26: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:54:31: 8000000 INFO @ Tue, 30 Jun 2020 02:54:33: 14000000 INFO @ Tue, 30 Jun 2020 02:54:38: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:54:39: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:54:39: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:54:39: #1 total tags in treatment: 14718503 INFO @ Tue, 30 Jun 2020 02:54:39: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:54:39: #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 02:54:40: #1 tags after filtering in treatment: 14718503 INFO @ Tue, 30 Jun 2020 02:54:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:54:40: #1 finished! INFO @ Tue, 30 Jun 2020 02:54:40: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:54:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:54:40: 9000000 INFO @ Tue, 30 Jun 2020 02:54:41: #2 number of paired peaks: 691 WARNING @ Tue, 30 Jun 2020 02:54:41: Fewer paired peaks (691) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 691 pairs to build model! INFO @ Tue, 30 Jun 2020 02:54:41: start model_add_line... INFO @ Tue, 30 Jun 2020 02:54:41: start X-correlation... INFO @ Tue, 30 Jun 2020 02:54:41: end of X-cor INFO @ Tue, 30 Jun 2020 02:54:41: #2 finished! INFO @ Tue, 30 Jun 2020 02:54:41: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:54:41: #2 alternative fragment length(s) may be 2,24 bps INFO @ Tue, 30 Jun 2020 02:54:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX481091/SRX481091.10_model.r WARNING @ Tue, 30 Jun 2020 02:54:41: #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 02:54:41: #2 You may need to consider one of the other alternative d(s): 2,24 WARNING @ Tue, 30 Jun 2020 02:54:41: #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 02:54:41: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:54:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:54:48: 10000000 INFO @ Tue, 30 Jun 2020 02:54:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX481091/SRX481091.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:54:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX481091/SRX481091.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:54:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX481091/SRX481091.05_summits.bed INFO @ Tue, 30 Jun 2020 02:54:53: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:54:55: 11000000 INFO @ Tue, 30 Jun 2020 02:55:04: 12000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:55:11: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:55:12: 13000000 INFO @ Tue, 30 Jun 2020 02:55:19: 14000000 INFO @ Tue, 30 Jun 2020 02:55:25: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:55:25: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:55:25: #1 total tags in treatment: 14718503 INFO @ Tue, 30 Jun 2020 02:55:25: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:55:25: #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 02:55:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX481091/SRX481091.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:55:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX481091/SRX481091.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:55:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX481091/SRX481091.10_summits.bed INFO @ Tue, 30 Jun 2020 02:55:25: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:55:26: #1 tags after filtering in treatment: 14718503 INFO @ Tue, 30 Jun 2020 02:55:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:55:26: #1 finished! INFO @ Tue, 30 Jun 2020 02:55:26: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:55:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:55:27: #2 number of paired peaks: 691 WARNING @ Tue, 30 Jun 2020 02:55:27: Fewer paired peaks (691) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 691 pairs to build model! INFO @ Tue, 30 Jun 2020 02:55:27: start model_add_line... INFO @ Tue, 30 Jun 2020 02:55:27: start X-correlation... INFO @ Tue, 30 Jun 2020 02:55:27: end of X-cor INFO @ Tue, 30 Jun 2020 02:55:27: #2 finished! INFO @ Tue, 30 Jun 2020 02:55:27: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:55:27: #2 alternative fragment length(s) may be 2,24 bps INFO @ Tue, 30 Jun 2020 02:55:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX481091/SRX481091.20_model.r WARNING @ Tue, 30 Jun 2020 02:55:27: #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 02:55:27: #2 You may need to consider one of the other alternative d(s): 2,24 WARNING @ Tue, 30 Jun 2020 02:55:27: #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 02:55:27: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:55:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:55:58: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:56:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX481091/SRX481091.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:56:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX481091/SRX481091.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:56:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX481091/SRX481091.20_summits.bed INFO @ Tue, 30 Jun 2020 02:56:12: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling