Job ID = 6455013 SRX = SRX2618558 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:33:55 prefetch.2.10.7: 1) Downloading 'SRR5319112'... 2020-06-21T09:33:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:36:21 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:36:22 prefetch.2.10.7: 'SRR5319112' is valid 2020-06-21T09:36:22 prefetch.2.10.7: 1) 'SRR5319112' was downloaded successfully 2020-06-21T09:36:22 prefetch.2.10.7: 'SRR5319112' has 0 unresolved dependencies Read 21028076 spots for SRR5319112/SRR5319112.sra Written 21028076 spots for SRR5319112/SRR5319112.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: 00:06:17 21028076 reads; of these: 21028076 (100.00%) were unpaired; of these: 984708 (4.68%) aligned 0 times 14682512 (69.82%) aligned exactly 1 time 5360856 (25.49%) aligned >1 times 95.32% overall alignment rate Time searching: 00:06:17 Overall time: 00:06:17 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] 3107061 / 20043368 = 0.1550 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 @ Sun, 21 Jun 2020 18:49:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618558/SRX2618558.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618558/SRX2618558.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618558/SRX2618558.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618558/SRX2618558.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 @ Sun, 21 Jun 2020 18:49:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:49:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:49:50: 1000000 INFO @ Sun, 21 Jun 2020 18:49:57: 2000000 INFO @ Sun, 21 Jun 2020 18:50:04: 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 @ Sun, 21 Jun 2020 18:50:10: 4000000 INFO @ Sun, 21 Jun 2020 18:50:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618558/SRX2618558.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618558/SRX2618558.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618558/SRX2618558.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618558/SRX2618558.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 @ Sun, 21 Jun 2020 18:50:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:50:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:50:17: 5000000 INFO @ Sun, 21 Jun 2020 18:50:20: 1000000 INFO @ Sun, 21 Jun 2020 18:50:24: 6000000 INFO @ Sun, 21 Jun 2020 18:50:27: 2000000 INFO @ Sun, 21 Jun 2020 18:50:31: 7000000 INFO @ Sun, 21 Jun 2020 18:50:35: 3000000 INFO @ Sun, 21 Jun 2020 18:50:39: 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 @ Sun, 21 Jun 2020 18:50:42: 4000000 INFO @ Sun, 21 Jun 2020 18:50:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618558/SRX2618558.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618558/SRX2618558.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618558/SRX2618558.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618558/SRX2618558.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 @ Sun, 21 Jun 2020 18:50:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:50:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:50:46: 9000000 INFO @ Sun, 21 Jun 2020 18:50:49: 5000000 INFO @ Sun, 21 Jun 2020 18:50:50: 1000000 INFO @ Sun, 21 Jun 2020 18:50:53: 10000000 INFO @ Sun, 21 Jun 2020 18:50:56: 6000000 INFO @ Sun, 21 Jun 2020 18:50:58: 2000000 INFO @ Sun, 21 Jun 2020 18:51:00: 11000000 INFO @ Sun, 21 Jun 2020 18:51:03: 7000000 INFO @ Sun, 21 Jun 2020 18:51:05: 3000000 INFO @ Sun, 21 Jun 2020 18:51:07: 12000000 INFO @ Sun, 21 Jun 2020 18:51:11: 8000000 INFO @ Sun, 21 Jun 2020 18:51:12: 4000000 INFO @ Sun, 21 Jun 2020 18:51:14: 13000000 INFO @ Sun, 21 Jun 2020 18:51:18: 9000000 INFO @ Sun, 21 Jun 2020 18:51:19: 5000000 INFO @ Sun, 21 Jun 2020 18:51:22: 14000000 INFO @ Sun, 21 Jun 2020 18:51:25: 10000000 INFO @ Sun, 21 Jun 2020 18:51:26: 6000000 INFO @ Sun, 21 Jun 2020 18:51:29: 15000000 INFO @ Sun, 21 Jun 2020 18:51:32: 11000000 INFO @ Sun, 21 Jun 2020 18:51:33: 7000000 INFO @ Sun, 21 Jun 2020 18:51:36: 16000000 INFO @ Sun, 21 Jun 2020 18:51:39: 12000000 INFO @ Sun, 21 Jun 2020 18:51:41: 8000000 INFO @ Sun, 21 Jun 2020 18:51:44: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:51:44: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:51:44: #1 total tags in treatment: 16936307 INFO @ Sun, 21 Jun 2020 18:51:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:51:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:51:45: #1 tags after filtering in treatment: 16936305 INFO @ Sun, 21 Jun 2020 18:51:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:51:45: #1 finished! INFO @ Sun, 21 Jun 2020 18:51:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:51:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:51:46: #2 number of paired peaks: 944 WARNING @ Sun, 21 Jun 2020 18:51:46: Fewer paired peaks (944) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 944 pairs to build model! INFO @ Sun, 21 Jun 2020 18:51:46: start model_add_line... INFO @ Sun, 21 Jun 2020 18:51:46: 13000000 INFO @ Sun, 21 Jun 2020 18:51:46: start X-correlation... INFO @ Sun, 21 Jun 2020 18:51:46: end of X-cor INFO @ Sun, 21 Jun 2020 18:51:46: #2 finished! INFO @ Sun, 21 Jun 2020 18:51:46: #2 predicted fragment length is 80 bps INFO @ Sun, 21 Jun 2020 18:51:46: #2 alternative fragment length(s) may be 80 bps INFO @ Sun, 21 Jun 2020 18:51:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618558/SRX2618558.05_model.r WARNING @ Sun, 21 Jun 2020 18:51:46: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:51:46: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Sun, 21 Jun 2020 18:51:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:51:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:51:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:51:48: 9000000 INFO @ Sun, 21 Jun 2020 18:51:53: 14000000 INFO @ Sun, 21 Jun 2020 18:51:54: 10000000 INFO @ Sun, 21 Jun 2020 18:51:59: 15000000 INFO @ Sun, 21 Jun 2020 18:52:01: 11000000 INFO @ Sun, 21 Jun 2020 18:52:05: 16000000 INFO @ Sun, 21 Jun 2020 18:52:08: 12000000 INFO @ Sun, 21 Jun 2020 18:52:12: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:52:12: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:52:12: #1 total tags in treatment: 16936307 INFO @ Sun, 21 Jun 2020 18:52:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:52:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:52:13: #1 tags after filtering in treatment: 16936305 INFO @ Sun, 21 Jun 2020 18:52:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:52:13: #1 finished! INFO @ Sun, 21 Jun 2020 18:52:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:52:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:52:14: #2 number of paired peaks: 944 WARNING @ Sun, 21 Jun 2020 18:52:14: Fewer paired peaks (944) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 944 pairs to build model! INFO @ Sun, 21 Jun 2020 18:52:14: start model_add_line... INFO @ Sun, 21 Jun 2020 18:52:15: start X-correlation... INFO @ Sun, 21 Jun 2020 18:52:15: end of X-cor INFO @ Sun, 21 Jun 2020 18:52:15: #2 finished! INFO @ Sun, 21 Jun 2020 18:52:15: #2 predicted fragment length is 80 bps INFO @ Sun, 21 Jun 2020 18:52:15: #2 alternative fragment length(s) may be 80 bps INFO @ Sun, 21 Jun 2020 18:52:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618558/SRX2618558.10_model.r WARNING @ Sun, 21 Jun 2020 18:52:15: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:52:15: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Sun, 21 Jun 2020 18:52:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:52:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:52:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:52:15: 13000000 INFO @ Sun, 21 Jun 2020 18:52:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:52:23: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:52:29: 15000000 INFO @ Sun, 21 Jun 2020 18:52:36: 16000000 INFO @ Sun, 21 Jun 2020 18:52:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618558/SRX2618558.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:52:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618558/SRX2618558.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:52:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618558/SRX2618558.05_summits.bed INFO @ Sun, 21 Jun 2020 18:52:37: Done! pass1 - making usageList (682 chroms): 3 millis pass2 - checking and writing primary data (8631 records, 4 fields): 48 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:52:43: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:52:43: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:52:43: #1 total tags in treatment: 16936307 INFO @ Sun, 21 Jun 2020 18:52:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:52:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:52:44: #1 tags after filtering in treatment: 16936305 INFO @ Sun, 21 Jun 2020 18:52:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:52:44: #1 finished! INFO @ Sun, 21 Jun 2020 18:52:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:52:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:52:45: #2 number of paired peaks: 944 WARNING @ Sun, 21 Jun 2020 18:52:45: Fewer paired peaks (944) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 944 pairs to build model! INFO @ Sun, 21 Jun 2020 18:52:45: start model_add_line... INFO @ Sun, 21 Jun 2020 18:52:45: start X-correlation... INFO @ Sun, 21 Jun 2020 18:52:45: end of X-cor INFO @ Sun, 21 Jun 2020 18:52:45: #2 finished! INFO @ Sun, 21 Jun 2020 18:52:45: #2 predicted fragment length is 80 bps INFO @ Sun, 21 Jun 2020 18:52:45: #2 alternative fragment length(s) may be 80 bps INFO @ Sun, 21 Jun 2020 18:52:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618558/SRX2618558.20_model.r WARNING @ Sun, 21 Jun 2020 18:52:45: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:52:45: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Sun, 21 Jun 2020 18:52:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:52:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:52:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:52:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:53:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618558/SRX2618558.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:53:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618558/SRX2618558.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:53:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618558/SRX2618558.10_summits.bed INFO @ Sun, 21 Jun 2020 18:53:05: Done! pass1 - making usageList (590 chroms): 2 millis pass2 - checking and writing primary data (6735 records, 4 fields): 38 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:53:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:53:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618558/SRX2618558.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:53:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618558/SRX2618558.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:53:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618558/SRX2618558.20_summits.bed INFO @ Sun, 21 Jun 2020 18:53:36: Done! pass1 - making usageList (469 chroms): 2 millis pass2 - checking and writing primary data (3326 records, 4 fields): 28 millis CompletedMACS2peakCalling