Job ID = 6527483 SRX = SRX026868 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T12:26:19 prefetch.2.10.7: 1) Downloading 'SRR065770'... 2020-06-29T12:26:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:28:35 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:28:36 prefetch.2.10.7: 'SRR065770' is valid 2020-06-29T12:28:36 prefetch.2.10.7: 1) 'SRR065770' was downloaded successfully Read 23509855 spots for SRR065770/SRR065770.sra Written 23509855 spots for SRR065770/SRR065770.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: 00:07:29 23509855 reads; of these: 23509855 (100.00%) were unpaired; of these: 475464 (2.02%) aligned 0 times 14397696 (61.24%) aligned exactly 1 time 8636695 (36.74%) aligned >1 times 97.98% overall alignment rate Time searching: 00:07:29 Overall time: 00:07:29 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 8 files... [bam_rmdupse_core] 6252011 / 23034391 = 0.2714 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 21:44:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX026868/SRX026868.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX026868/SRX026868.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX026868/SRX026868.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX026868/SRX026868.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 21:44:46: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:44:46: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:44:51: 1000000 INFO @ Mon, 29 Jun 2020 21:44:56: 2000000 INFO @ Mon, 29 Jun 2020 21:45:02: 3000000 INFO @ Mon, 29 Jun 2020 21:45:07: 4000000 INFO @ Mon, 29 Jun 2020 21:45:13: 5000000 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 21:45:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX026868/SRX026868.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX026868/SRX026868.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX026868/SRX026868.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX026868/SRX026868.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 21:45:16: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:45:16: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:45:19: 6000000 INFO @ Mon, 29 Jun 2020 21:45:22: 1000000 INFO @ Mon, 29 Jun 2020 21:45:26: 7000000 INFO @ Mon, 29 Jun 2020 21:45:29: 2000000 INFO @ Mon, 29 Jun 2020 21:45:32: 8000000 INFO @ Mon, 29 Jun 2020 21:45:35: 3000000 INFO @ Mon, 29 Jun 2020 21:45:38: 9000000 INFO @ Mon, 29 Jun 2020 21:45:42: 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 @ Mon, 29 Jun 2020 21:45:45: 10000000 INFO @ Mon, 29 Jun 2020 21:45:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX026868/SRX026868.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX026868/SRX026868.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX026868/SRX026868.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX026868/SRX026868.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 21:45:46: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:45:46: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:45:48: 5000000 INFO @ Mon, 29 Jun 2020 21:45:51: 11000000 INFO @ Mon, 29 Jun 2020 21:45:53: 1000000 INFO @ Mon, 29 Jun 2020 21:45:55: 6000000 INFO @ Mon, 29 Jun 2020 21:45:58: 12000000 INFO @ Mon, 29 Jun 2020 21:46:00: 2000000 INFO @ Mon, 29 Jun 2020 21:46:03: 7000000 INFO @ Mon, 29 Jun 2020 21:46:05: 13000000 INFO @ Mon, 29 Jun 2020 21:46:07: 3000000 INFO @ Mon, 29 Jun 2020 21:46:10: 8000000 INFO @ Mon, 29 Jun 2020 21:46:12: 14000000 INFO @ Mon, 29 Jun 2020 21:46:14: 4000000 INFO @ Mon, 29 Jun 2020 21:46:17: 9000000 INFO @ Mon, 29 Jun 2020 21:46:18: 15000000 INFO @ Mon, 29 Jun 2020 21:46:22: 5000000 INFO @ Mon, 29 Jun 2020 21:46:24: 10000000 INFO @ Mon, 29 Jun 2020 21:46:25: 16000000 INFO @ Mon, 29 Jun 2020 21:46:29: 6000000 INFO @ Mon, 29 Jun 2020 21:46:31: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 21:46:31: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 21:46:31: #1 total tags in treatment: 16782380 INFO @ Mon, 29 Jun 2020 21:46:31: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:46:31: #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 21:46:31: 11000000 INFO @ Mon, 29 Jun 2020 21:46:31: #1 tags after filtering in treatment: 16782380 INFO @ Mon, 29 Jun 2020 21:46:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:46:31: #1 finished! INFO @ Mon, 29 Jun 2020 21:46:31: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:46:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:46:32: #2 number of paired peaks: 351 WARNING @ Mon, 29 Jun 2020 21:46:32: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Mon, 29 Jun 2020 21:46:32: start model_add_line... INFO @ Mon, 29 Jun 2020 21:46:32: start X-correlation... INFO @ Mon, 29 Jun 2020 21:46:32: end of X-cor INFO @ Mon, 29 Jun 2020 21:46:32: #2 finished! INFO @ Mon, 29 Jun 2020 21:46:32: #2 predicted fragment length is 36 bps INFO @ Mon, 29 Jun 2020 21:46:32: #2 alternative fragment length(s) may be 36 bps INFO @ Mon, 29 Jun 2020 21:46:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX026868/SRX026868.05_model.r WARNING @ Mon, 29 Jun 2020 21:46:32: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 21:46:32: #2 You may need to consider one of the other alternative d(s): 36 WARNING @ Mon, 29 Jun 2020 21:46:32: #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 21:46:32: #3 Call peaks... INFO @ Mon, 29 Jun 2020 21:46:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 21:46:36: 7000000 INFO @ Mon, 29 Jun 2020 21:46:38: 12000000 INFO @ Mon, 29 Jun 2020 21:46:43: 8000000 INFO @ Mon, 29 Jun 2020 21:46:45: 13000000 INFO @ Mon, 29 Jun 2020 21:46:50: 9000000 INFO @ Mon, 29 Jun 2020 21:46:52: 14000000 INFO @ Mon, 29 Jun 2020 21:46:57: 10000000 INFO @ Mon, 29 Jun 2020 21:46:58: 15000000 INFO @ Mon, 29 Jun 2020 21:47:04: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 21:47:04: 11000000 INFO @ Mon, 29 Jun 2020 21:47:05: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 21:47:10: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 21:47:10: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 21:47:10: #1 total tags in treatment: 16782380 INFO @ Mon, 29 Jun 2020 21:47:10: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:47:10: #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 21:47:11: #1 tags after filtering in treatment: 16782380 INFO @ Mon, 29 Jun 2020 21:47:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:47:11: #1 finished! INFO @ Mon, 29 Jun 2020 21:47:11: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:47:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:47:11: 12000000 INFO @ Mon, 29 Jun 2020 21:47:12: #2 number of paired peaks: 351 WARNING @ Mon, 29 Jun 2020 21:47:12: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Mon, 29 Jun 2020 21:47:12: start model_add_line... INFO @ Mon, 29 Jun 2020 21:47:12: start X-correlation... INFO @ Mon, 29 Jun 2020 21:47:12: end of X-cor INFO @ Mon, 29 Jun 2020 21:47:12: #2 finished! INFO @ Mon, 29 Jun 2020 21:47:12: #2 predicted fragment length is 36 bps INFO @ Mon, 29 Jun 2020 21:47:12: #2 alternative fragment length(s) may be 36 bps INFO @ Mon, 29 Jun 2020 21:47:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX026868/SRX026868.10_model.r WARNING @ Mon, 29 Jun 2020 21:47:12: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 21:47:12: #2 You may need to consider one of the other alternative d(s): 36 WARNING @ Mon, 29 Jun 2020 21:47:12: #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 21:47:12: #3 Call peaks... INFO @ Mon, 29 Jun 2020 21:47:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 21:47:18: 13000000 INFO @ Mon, 29 Jun 2020 21:47:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX026868/SRX026868.05_peaks.xls INFO @ Mon, 29 Jun 2020 21:47:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX026868/SRX026868.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 21:47:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX026868/SRX026868.05_summits.bed INFO @ Mon, 29 Jun 2020 21:47:20: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2122 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 21:47:24: 14000000 INFO @ Mon, 29 Jun 2020 21:47:31: 15000000 INFO @ Mon, 29 Jun 2020 21:47:37: 16000000 BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 21:47:42: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 21:47:42: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 21:47:42: #1 total tags in treatment: 16782380 INFO @ Mon, 29 Jun 2020 21:47:42: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:47:42: #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 21:47:43: #1 tags after filtering in treatment: 16782380 INFO @ Mon, 29 Jun 2020 21:47:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:47:43: #1 finished! INFO @ Mon, 29 Jun 2020 21:47:43: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:47:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:47:43: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 21:47:44: #2 number of paired peaks: 351 WARNING @ Mon, 29 Jun 2020 21:47:44: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Mon, 29 Jun 2020 21:47:44: start model_add_line... INFO @ Mon, 29 Jun 2020 21:47:44: start X-correlation... INFO @ Mon, 29 Jun 2020 21:47:44: end of X-cor INFO @ Mon, 29 Jun 2020 21:47:44: #2 finished! INFO @ Mon, 29 Jun 2020 21:47:44: #2 predicted fragment length is 36 bps INFO @ Mon, 29 Jun 2020 21:47:44: #2 alternative fragment length(s) may be 36 bps INFO @ Mon, 29 Jun 2020 21:47:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX026868/SRX026868.20_model.r WARNING @ Mon, 29 Jun 2020 21:47:44: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 21:47:44: #2 You may need to consider one of the other alternative d(s): 36 WARNING @ Mon, 29 Jun 2020 21:47:44: #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 21:47:44: #3 Call peaks... INFO @ Mon, 29 Jun 2020 21:47:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 21:47:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX026868/SRX026868.10_peaks.xls INFO @ Mon, 29 Jun 2020 21:47:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX026868/SRX026868.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 21:47:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX026868/SRX026868.10_summits.bed INFO @ Mon, 29 Jun 2020 21:47:58: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1821 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 21:48:14: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 21:48:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX026868/SRX026868.20_peaks.xls INFO @ Mon, 29 Jun 2020 21:48:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX026868/SRX026868.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 21:48:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX026868/SRX026868.20_summits.bed INFO @ Mon, 29 Jun 2020 21:48:30: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1193 records, 4 fields): 2 millis CompletedMACS2peakCalling