Job ID = 6528081 SRX = SRX4158163 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T14:15:50 prefetch.2.10.7: 1) Downloading 'SRR7253443'... 2020-06-29T14:15:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:17:40 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:17:40 prefetch.2.10.7: 1) 'SRR7253443' was downloaded successfully Read 23284404 spots for SRR7253443/SRR7253443.sra Written 23284404 spots for SRR7253443/SRR7253443.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: 00:00:00 Multiseed full-index search: 00:09:06 23284404 reads; of these: 23284404 (100.00%) were unpaired; of these: 857662 (3.68%) aligned 0 times 13035550 (55.98%) aligned exactly 1 time 9391192 (40.33%) aligned >1 times 96.32% overall alignment rate Time searching: 00:09:06 Overall time: 00:09:06 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 12 files... [bam_rmdupse_core] 3247460 / 22426742 = 0.1448 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 @ Mon, 29 Jun 2020 23:42:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158163/SRX4158163.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158163/SRX4158163.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158163/SRX4158163.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158163/SRX4158163.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 @ Mon, 29 Jun 2020 23:42:20: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:42:20: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:42:26: 1000000 INFO @ Mon, 29 Jun 2020 23:42:31: 2000000 INFO @ Mon, 29 Jun 2020 23:42:36: 3000000 INFO @ Mon, 29 Jun 2020 23:42:42: 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 @ Mon, 29 Jun 2020 23:42:47: 5000000 INFO @ Mon, 29 Jun 2020 23:42:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158163/SRX4158163.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158163/SRX4158163.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158163/SRX4158163.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158163/SRX4158163.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 @ Mon, 29 Jun 2020 23:42:49: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:42:49: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:42:53: 6000000 INFO @ Mon, 29 Jun 2020 23:42:56: 1000000 INFO @ Mon, 29 Jun 2020 23:42:59: 7000000 INFO @ Mon, 29 Jun 2020 23:43:02: 2000000 INFO @ Mon, 29 Jun 2020 23:43:05: 8000000 INFO @ Mon, 29 Jun 2020 23:43:08: 3000000 INFO @ Mon, 29 Jun 2020 23:43:11: 9000000 INFO @ Mon, 29 Jun 2020 23:43:14: 4000000 BedGraph に変換中... INFO @ Mon, 29 Jun 2020 23:43:17: 10000000 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 @ Mon, 29 Jun 2020 23:43:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158163/SRX4158163.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158163/SRX4158163.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158163/SRX4158163.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158163/SRX4158163.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 @ Mon, 29 Jun 2020 23:43:19: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:43:19: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:43:20: 5000000 INFO @ Mon, 29 Jun 2020 23:43:23: 11000000 INFO @ Mon, 29 Jun 2020 23:43:26: 1000000 INFO @ Mon, 29 Jun 2020 23:43:27: 6000000 INFO @ Mon, 29 Jun 2020 23:43:30: 12000000 INFO @ Mon, 29 Jun 2020 23:43:33: 2000000 INFO @ Mon, 29 Jun 2020 23:43:33: 7000000 INFO @ Mon, 29 Jun 2020 23:43:36: 13000000 INFO @ Mon, 29 Jun 2020 23:43:39: 3000000 INFO @ Mon, 29 Jun 2020 23:43:40: 8000000 INFO @ Mon, 29 Jun 2020 23:43:42: 14000000 INFO @ Mon, 29 Jun 2020 23:43:45: 4000000 INFO @ Mon, 29 Jun 2020 23:43:46: 9000000 INFO @ Mon, 29 Jun 2020 23:43:49: 15000000 INFO @ Mon, 29 Jun 2020 23:43:51: 5000000 INFO @ Mon, 29 Jun 2020 23:43:52: 10000000 INFO @ Mon, 29 Jun 2020 23:43:55: 16000000 INFO @ Mon, 29 Jun 2020 23:43:57: 6000000 INFO @ Mon, 29 Jun 2020 23:43:59: 11000000 INFO @ Mon, 29 Jun 2020 23:44:01: 17000000 INFO @ Mon, 29 Jun 2020 23:44:02: 7000000 INFO @ Mon, 29 Jun 2020 23:44:05: 12000000 INFO @ Mon, 29 Jun 2020 23:44:07: 18000000 INFO @ Mon, 29 Jun 2020 23:44:08: 8000000 INFO @ Mon, 29 Jun 2020 23:44:11: 13000000 INFO @ Mon, 29 Jun 2020 23:44:13: 9000000 INFO @ Mon, 29 Jun 2020 23:44:13: 19000000 INFO @ Mon, 29 Jun 2020 23:44:15: #1 tag size is determined as 49 bps INFO @ Mon, 29 Jun 2020 23:44:15: #1 tag size = 49 INFO @ Mon, 29 Jun 2020 23:44:15: #1 total tags in treatment: 19179282 INFO @ Mon, 29 Jun 2020 23:44:15: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:44:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:44:15: #1 tags after filtering in treatment: 19179282 INFO @ Mon, 29 Jun 2020 23:44:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:44:15: #1 finished! INFO @ Mon, 29 Jun 2020 23:44:15: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:44:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:44:16: #2 number of paired peaks: 178 WARNING @ Mon, 29 Jun 2020 23:44:16: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Mon, 29 Jun 2020 23:44:16: start model_add_line... INFO @ Mon, 29 Jun 2020 23:44:16: start X-correlation... INFO @ Mon, 29 Jun 2020 23:44:16: end of X-cor INFO @ Mon, 29 Jun 2020 23:44:16: #2 finished! INFO @ Mon, 29 Jun 2020 23:44:16: #2 predicted fragment length is 2 bps INFO @ Mon, 29 Jun 2020 23:44:16: #2 alternative fragment length(s) may be 2,29,49,551 bps INFO @ Mon, 29 Jun 2020 23:44:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158163/SRX4158163.05_model.r WARNING @ Mon, 29 Jun 2020 23:44:16: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:44:16: #2 You may need to consider one of the other alternative d(s): 2,29,49,551 WARNING @ Mon, 29 Jun 2020 23:44:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:44:16: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:44:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:44:17: 14000000 INFO @ Mon, 29 Jun 2020 23:44:19: 10000000 INFO @ Mon, 29 Jun 2020 23:44:23: 15000000 INFO @ Mon, 29 Jun 2020 23:44:24: 11000000 INFO @ Mon, 29 Jun 2020 23:44:28: 16000000 INFO @ Mon, 29 Jun 2020 23:44:29: 12000000 INFO @ Mon, 29 Jun 2020 23:44:34: 17000000 INFO @ Mon, 29 Jun 2020 23:44:34: 13000000 INFO @ Mon, 29 Jun 2020 23:44:40: 14000000 INFO @ Mon, 29 Jun 2020 23:44:40: 18000000 INFO @ Mon, 29 Jun 2020 23:44:45: 15000000 INFO @ Mon, 29 Jun 2020 23:44:46: 19000000 INFO @ Mon, 29 Jun 2020 23:44:47: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:44:47: #1 tag size is determined as 49 bps INFO @ Mon, 29 Jun 2020 23:44:47: #1 tag size = 49 INFO @ Mon, 29 Jun 2020 23:44:47: #1 total tags in treatment: 19179282 INFO @ Mon, 29 Jun 2020 23:44:47: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:44:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:44:47: #1 tags after filtering in treatment: 19179282 INFO @ Mon, 29 Jun 2020 23:44:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:44:47: #1 finished! INFO @ Mon, 29 Jun 2020 23:44:47: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:44:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:44:49: #2 number of paired peaks: 178 WARNING @ Mon, 29 Jun 2020 23:44:49: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Mon, 29 Jun 2020 23:44:49: start model_add_line... INFO @ Mon, 29 Jun 2020 23:44:49: start X-correlation... INFO @ Mon, 29 Jun 2020 23:44:49: end of X-cor INFO @ Mon, 29 Jun 2020 23:44:49: #2 finished! INFO @ Mon, 29 Jun 2020 23:44:49: #2 predicted fragment length is 2 bps INFO @ Mon, 29 Jun 2020 23:44:49: #2 alternative fragment length(s) may be 2,29,49,551 bps INFO @ Mon, 29 Jun 2020 23:44:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158163/SRX4158163.10_model.r WARNING @ Mon, 29 Jun 2020 23:44:49: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:44:49: #2 You may need to consider one of the other alternative d(s): 2,29,49,551 WARNING @ Mon, 29 Jun 2020 23:44:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:44:49: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:44:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:44:50: 16000000 INFO @ Mon, 29 Jun 2020 23:44:55: 17000000 INFO @ Mon, 29 Jun 2020 23:45:01: 18000000 INFO @ Mon, 29 Jun 2020 23:45:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158163/SRX4158163.05_peaks.xls INFO @ Mon, 29 Jun 2020 23:45:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158163/SRX4158163.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:45:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158163/SRX4158163.05_summits.bed INFO @ Mon, 29 Jun 2020 23:45:01: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:45:06: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:45:07: #1 tag size is determined as 49 bps INFO @ Mon, 29 Jun 2020 23:45:07: #1 tag size = 49 INFO @ Mon, 29 Jun 2020 23:45:07: #1 total tags in treatment: 19179282 INFO @ Mon, 29 Jun 2020 23:45:07: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:45:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:45:07: #1 tags after filtering in treatment: 19179282 INFO @ Mon, 29 Jun 2020 23:45:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:45:07: #1 finished! INFO @ Mon, 29 Jun 2020 23:45:07: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:45:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:45:09: #2 number of paired peaks: 178 WARNING @ Mon, 29 Jun 2020 23:45:09: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Mon, 29 Jun 2020 23:45:09: start model_add_line... INFO @ Mon, 29 Jun 2020 23:45:09: start X-correlation... INFO @ Mon, 29 Jun 2020 23:45:09: end of X-cor INFO @ Mon, 29 Jun 2020 23:45:09: #2 finished! INFO @ Mon, 29 Jun 2020 23:45:09: #2 predicted fragment length is 2 bps INFO @ Mon, 29 Jun 2020 23:45:09: #2 alternative fragment length(s) may be 2,29,49,551 bps INFO @ Mon, 29 Jun 2020 23:45:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158163/SRX4158163.20_model.r WARNING @ Mon, 29 Jun 2020 23:45:09: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:45:09: #2 You may need to consider one of the other alternative d(s): 2,29,49,551 WARNING @ Mon, 29 Jun 2020 23:45:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:45:09: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:45:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:45:19: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:45:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158163/SRX4158163.10_peaks.xls INFO @ Mon, 29 Jun 2020 23:45:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158163/SRX4158163.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:45:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158163/SRX4158163.10_summits.bed INFO @ Mon, 29 Jun 2020 23:45:34: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:45:39: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:45:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158163/SRX4158163.20_peaks.xls INFO @ Mon, 29 Jun 2020 23:45:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158163/SRX4158163.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:45:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158163/SRX4158163.20_summits.bed INFO @ Mon, 29 Jun 2020 23:45:53: 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。