Job ID = 6529448 SRX = SRX287572 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: 00:09:04 26924228 reads; of these: 26924228 (100.00%) were unpaired; of these: 1437606 (5.34%) aligned 0 times 17200607 (63.89%) aligned exactly 1 time 8286015 (30.78%) aligned >1 times 94.66% overall alignment rate Time searching: 00:09:04 Overall time: 00:09:04 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] 4923040 / 25486622 = 0.1932 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 02:20:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287572/SRX287572.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287572/SRX287572.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287572/SRX287572.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287572/SRX287572.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 02:20:42: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:20:42: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:20:49: 1000000 INFO @ Tue, 30 Jun 2020 02:20:56: 2000000 INFO @ Tue, 30 Jun 2020 02:21:02: 3000000 INFO @ Tue, 30 Jun 2020 02:21:09: 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 02:21:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287572/SRX287572.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287572/SRX287572.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287572/SRX287572.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287572/SRX287572.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 02:21:12: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:21:12: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:21:15: 5000000 INFO @ Tue, 30 Jun 2020 02:21:19: 1000000 INFO @ Tue, 30 Jun 2020 02:21:22: 6000000 INFO @ Tue, 30 Jun 2020 02:21:26: 2000000 INFO @ Tue, 30 Jun 2020 02:21:28: 7000000 INFO @ Tue, 30 Jun 2020 02:21:32: 3000000 INFO @ Tue, 30 Jun 2020 02:21:35: 8000000 INFO @ Tue, 30 Jun 2020 02:21:39: 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 02:21:41: 9000000 INFO @ Tue, 30 Jun 2020 02:21:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287572/SRX287572.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287572/SRX287572.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287572/SRX287572.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287572/SRX287572.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 02:21:42: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:21:42: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:21:45: 5000000 INFO @ Tue, 30 Jun 2020 02:21:48: 10000000 INFO @ Tue, 30 Jun 2020 02:21:49: 1000000 INFO @ Tue, 30 Jun 2020 02:21:52: 6000000 INFO @ Tue, 30 Jun 2020 02:21:55: 11000000 INFO @ Tue, 30 Jun 2020 02:21:56: 2000000 INFO @ Tue, 30 Jun 2020 02:21:59: 7000000 INFO @ Tue, 30 Jun 2020 02:22:02: 12000000 INFO @ Tue, 30 Jun 2020 02:22:03: 3000000 INFO @ Tue, 30 Jun 2020 02:22:06: 8000000 INFO @ Tue, 30 Jun 2020 02:22:09: 13000000 INFO @ Tue, 30 Jun 2020 02:22:09: 4000000 INFO @ Tue, 30 Jun 2020 02:22:13: 9000000 INFO @ Tue, 30 Jun 2020 02:22:16: 14000000 INFO @ Tue, 30 Jun 2020 02:22:16: 5000000 INFO @ Tue, 30 Jun 2020 02:22:20: 10000000 INFO @ Tue, 30 Jun 2020 02:22:22: 15000000 INFO @ Tue, 30 Jun 2020 02:22:23: 6000000 INFO @ Tue, 30 Jun 2020 02:22:26: 11000000 INFO @ Tue, 30 Jun 2020 02:22:29: 16000000 INFO @ Tue, 30 Jun 2020 02:22:29: 7000000 INFO @ Tue, 30 Jun 2020 02:22:33: 12000000 INFO @ Tue, 30 Jun 2020 02:22:36: 8000000 INFO @ Tue, 30 Jun 2020 02:22:37: 17000000 INFO @ Tue, 30 Jun 2020 02:22:40: 13000000 INFO @ Tue, 30 Jun 2020 02:22:43: 9000000 INFO @ Tue, 30 Jun 2020 02:22:43: 18000000 INFO @ Tue, 30 Jun 2020 02:22:47: 14000000 INFO @ Tue, 30 Jun 2020 02:22:49: 10000000 INFO @ Tue, 30 Jun 2020 02:22:50: 19000000 INFO @ Tue, 30 Jun 2020 02:22:53: 15000000 INFO @ Tue, 30 Jun 2020 02:22:56: 11000000 INFO @ Tue, 30 Jun 2020 02:22:57: 20000000 INFO @ Tue, 30 Jun 2020 02:23:00: 16000000 INFO @ Tue, 30 Jun 2020 02:23:01: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:23:01: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:23:01: #1 total tags in treatment: 20563582 INFO @ Tue, 30 Jun 2020 02:23:01: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:23:01: #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 02:23:01: #1 tags after filtering in treatment: 20563582 INFO @ Tue, 30 Jun 2020 02:23:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:23:01: #1 finished! INFO @ Tue, 30 Jun 2020 02:23:01: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:23:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:23:03: #2 number of paired peaks: 577 WARNING @ Tue, 30 Jun 2020 02:23:03: Fewer paired peaks (577) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 577 pairs to build model! INFO @ Tue, 30 Jun 2020 02:23:03: start model_add_line... INFO @ Tue, 30 Jun 2020 02:23:03: start X-correlation... INFO @ Tue, 30 Jun 2020 02:23:03: end of X-cor INFO @ Tue, 30 Jun 2020 02:23:03: #2 finished! INFO @ Tue, 30 Jun 2020 02:23:03: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:23:03: #2 alternative fragment length(s) may be 2 bps INFO @ Tue, 30 Jun 2020 02:23:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287572/SRX287572.05_model.r WARNING @ Tue, 30 Jun 2020 02:23:03: #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 02:23:03: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Tue, 30 Jun 2020 02:23:03: #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 02:23:03: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:23:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:23:03: 12000000 INFO @ Tue, 30 Jun 2020 02:23:07: 17000000 INFO @ Tue, 30 Jun 2020 02:23:09: 13000000 INFO @ Tue, 30 Jun 2020 02:23:14: 18000000 INFO @ Tue, 30 Jun 2020 02:23:16: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:23:20: 19000000 INFO @ Tue, 30 Jun 2020 02:23:23: 15000000 INFO @ Tue, 30 Jun 2020 02:23:27: 20000000 INFO @ Tue, 30 Jun 2020 02:23:29: 16000000 INFO @ Tue, 30 Jun 2020 02:23:31: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:23:31: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:23:31: #1 total tags in treatment: 20563582 INFO @ Tue, 30 Jun 2020 02:23:31: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:23:31: #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 02:23:32: #1 tags after filtering in treatment: 20563582 INFO @ Tue, 30 Jun 2020 02:23:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:23:32: #1 finished! INFO @ Tue, 30 Jun 2020 02:23:32: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:23:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:23:33: #2 number of paired peaks: 577 WARNING @ Tue, 30 Jun 2020 02:23:33: Fewer paired peaks (577) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 577 pairs to build model! INFO @ Tue, 30 Jun 2020 02:23:33: start model_add_line... INFO @ Tue, 30 Jun 2020 02:23:33: start X-correlation... INFO @ Tue, 30 Jun 2020 02:23:33: end of X-cor INFO @ Tue, 30 Jun 2020 02:23:33: #2 finished! INFO @ Tue, 30 Jun 2020 02:23:33: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:23:33: #2 alternative fragment length(s) may be 2 bps INFO @ Tue, 30 Jun 2020 02:23:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287572/SRX287572.10_model.r WARNING @ Tue, 30 Jun 2020 02:23:33: #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 02:23:33: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Tue, 30 Jun 2020 02:23:33: #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 02:23:33: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:23:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:23:37: 17000000 INFO @ Tue, 30 Jun 2020 02:23:38: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:23:43: 18000000 INFO @ Tue, 30 Jun 2020 02:23:49: 19000000 INFO @ Tue, 30 Jun 2020 02:23:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287572/SRX287572.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:23:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287572/SRX287572.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:23:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287572/SRX287572.05_summits.bed INFO @ Tue, 30 Jun 2020 02:23:56: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:23:56: 20000000 INFO @ Tue, 30 Jun 2020 02:24:00: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:24:00: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:24:00: #1 total tags in treatment: 20563582 INFO @ Tue, 30 Jun 2020 02:24:00: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:24:00: #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 02:24:00: #1 tags after filtering in treatment: 20563582 INFO @ Tue, 30 Jun 2020 02:24:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:24:00: #1 finished! INFO @ Tue, 30 Jun 2020 02:24:00: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:24:00: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:24:02: #2 number of paired peaks: 577 WARNING @ Tue, 30 Jun 2020 02:24:02: Fewer paired peaks (577) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 577 pairs to build model! INFO @ Tue, 30 Jun 2020 02:24:02: start model_add_line... INFO @ Tue, 30 Jun 2020 02:24:02: start X-correlation... INFO @ Tue, 30 Jun 2020 02:24:02: end of X-cor INFO @ Tue, 30 Jun 2020 02:24:02: #2 finished! INFO @ Tue, 30 Jun 2020 02:24:02: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:24:02: #2 alternative fragment length(s) may be 2 bps INFO @ Tue, 30 Jun 2020 02:24:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287572/SRX287572.20_model.r WARNING @ Tue, 30 Jun 2020 02:24:02: #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 02:24:02: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Tue, 30 Jun 2020 02:24:02: #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 02:24:02: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:24:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:24:09: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:24:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287572/SRX287572.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:24:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287572/SRX287572.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:24:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287572/SRX287572.10_summits.bed INFO @ Tue, 30 Jun 2020 02:24:26: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:24:38: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:24:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287572/SRX287572.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:24:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287572/SRX287572.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:24:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287572/SRX287572.20_summits.bed INFO @ Tue, 30 Jun 2020 02:24:56: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling