Job ID = 6528525 SRX = SRX969931 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T15:22:18 prefetch.2.10.7: 1) Downloading 'SRR1931647'... 2020-06-29T15:22:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T15:25:10 prefetch.2.10.7: HTTPS download succeed 2020-06-29T15:25:10 prefetch.2.10.7: 1) 'SRR1931647' was downloaded successfully Read 29782622 spots for SRR1931647/SRR1931647.sra Written 29782622 spots for SRR1931647/SRR1931647.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: 00:11:08 29782622 reads; of these: 29782622 (100.00%) were unpaired; of these: 1471547 (4.94%) aligned 0 times 19753193 (66.32%) aligned exactly 1 time 8557882 (28.73%) aligned >1 times 95.06% overall alignment rate Time searching: 00:11:08 Overall time: 00:11:08 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] 4044064 / 28311075 = 0.1428 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 00:50:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX969931/SRX969931.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX969931/SRX969931.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX969931/SRX969931.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX969931/SRX969931.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 00:50:50: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:50:50: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:50:57: 1000000 INFO @ Tue, 30 Jun 2020 00:51:04: 2000000 INFO @ Tue, 30 Jun 2020 00:51:11: 3000000 INFO @ Tue, 30 Jun 2020 00:51:18: 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 00:51:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX969931/SRX969931.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX969931/SRX969931.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX969931/SRX969931.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX969931/SRX969931.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 00:51:20: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:51:20: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:51:25: 5000000 INFO @ Tue, 30 Jun 2020 00:51:27: 1000000 INFO @ Tue, 30 Jun 2020 00:51:33: 6000000 INFO @ Tue, 30 Jun 2020 00:51:34: 2000000 INFO @ Tue, 30 Jun 2020 00:51:41: 7000000 INFO @ Tue, 30 Jun 2020 00:51:42: 3000000 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 00:51:49: 4000000 INFO @ Tue, 30 Jun 2020 00:51:49: 8000000 INFO @ Tue, 30 Jun 2020 00:51:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX969931/SRX969931.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX969931/SRX969931.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX969931/SRX969931.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX969931/SRX969931.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 00:51:50: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:51:50: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:51:56: 5000000 INFO @ Tue, 30 Jun 2020 00:51:56: 9000000 INFO @ Tue, 30 Jun 2020 00:51:57: 1000000 INFO @ Tue, 30 Jun 2020 00:52:03: 6000000 INFO @ Tue, 30 Jun 2020 00:52:04: 10000000 INFO @ Tue, 30 Jun 2020 00:52:04: 2000000 INFO @ Tue, 30 Jun 2020 00:52:10: 7000000 INFO @ Tue, 30 Jun 2020 00:52:11: 3000000 INFO @ Tue, 30 Jun 2020 00:52:11: 11000000 INFO @ Tue, 30 Jun 2020 00:52:17: 8000000 INFO @ Tue, 30 Jun 2020 00:52:18: 4000000 INFO @ Tue, 30 Jun 2020 00:52:19: 12000000 INFO @ Tue, 30 Jun 2020 00:52:24: 9000000 INFO @ Tue, 30 Jun 2020 00:52:25: 5000000 INFO @ Tue, 30 Jun 2020 00:52:27: 13000000 INFO @ Tue, 30 Jun 2020 00:52:31: 10000000 INFO @ Tue, 30 Jun 2020 00:52:32: 6000000 INFO @ Tue, 30 Jun 2020 00:52:34: 14000000 INFO @ Tue, 30 Jun 2020 00:52:38: 11000000 INFO @ Tue, 30 Jun 2020 00:52:39: 7000000 INFO @ Tue, 30 Jun 2020 00:52:42: 15000000 INFO @ Tue, 30 Jun 2020 00:52:45: 12000000 INFO @ Tue, 30 Jun 2020 00:52:46: 8000000 INFO @ Tue, 30 Jun 2020 00:52:50: 16000000 INFO @ Tue, 30 Jun 2020 00:52:51: 13000000 INFO @ Tue, 30 Jun 2020 00:52:53: 9000000 INFO @ Tue, 30 Jun 2020 00:52:58: 17000000 INFO @ Tue, 30 Jun 2020 00:52:58: 14000000 INFO @ Tue, 30 Jun 2020 00:53:00: 10000000 INFO @ Tue, 30 Jun 2020 00:53:05: 18000000 INFO @ Tue, 30 Jun 2020 00:53:05: 15000000 INFO @ Tue, 30 Jun 2020 00:53:07: 11000000 INFO @ Tue, 30 Jun 2020 00:53:12: 16000000 INFO @ Tue, 30 Jun 2020 00:53:13: 19000000 INFO @ Tue, 30 Jun 2020 00:53:14: 12000000 INFO @ Tue, 30 Jun 2020 00:53:19: 17000000 INFO @ Tue, 30 Jun 2020 00:53:20: 20000000 INFO @ Tue, 30 Jun 2020 00:53:21: 13000000 INFO @ Tue, 30 Jun 2020 00:53:26: 18000000 INFO @ Tue, 30 Jun 2020 00:53:28: 14000000 INFO @ Tue, 30 Jun 2020 00:53:28: 21000000 INFO @ Tue, 30 Jun 2020 00:53:33: 19000000 INFO @ Tue, 30 Jun 2020 00:53:35: 15000000 INFO @ Tue, 30 Jun 2020 00:53:36: 22000000 INFO @ Tue, 30 Jun 2020 00:53:40: 20000000 INFO @ Tue, 30 Jun 2020 00:53:41: 16000000 INFO @ Tue, 30 Jun 2020 00:53:44: 23000000 INFO @ Tue, 30 Jun 2020 00:53:47: 21000000 INFO @ Tue, 30 Jun 2020 00:53:48: 17000000 INFO @ Tue, 30 Jun 2020 00:53:52: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 00:53:54: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:53:54: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:53:54: #1 total tags in treatment: 24267011 INFO @ Tue, 30 Jun 2020 00:53:54: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:53:54: #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 00:53:54: 22000000 INFO @ Tue, 30 Jun 2020 00:53:54: #1 tags after filtering in treatment: 24267011 INFO @ Tue, 30 Jun 2020 00:53:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:53:54: #1 finished! INFO @ Tue, 30 Jun 2020 00:53:54: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:53:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:53:55: 18000000 INFO @ Tue, 30 Jun 2020 00:53:56: #2 number of paired peaks: 113 WARNING @ Tue, 30 Jun 2020 00:53:56: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Tue, 30 Jun 2020 00:53:56: start model_add_line... INFO @ Tue, 30 Jun 2020 00:53:56: start X-correlation... INFO @ Tue, 30 Jun 2020 00:53:56: end of X-cor INFO @ Tue, 30 Jun 2020 00:53:56: #2 finished! INFO @ Tue, 30 Jun 2020 00:53:56: #2 predicted fragment length is 46 bps INFO @ Tue, 30 Jun 2020 00:53:56: #2 alternative fragment length(s) may be 46 bps INFO @ Tue, 30 Jun 2020 00:53:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX969931/SRX969931.05_model.r WARNING @ Tue, 30 Jun 2020 00:53:56: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:53:56: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Tue, 30 Jun 2020 00:53:56: #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 00:53:56: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:53:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:54:01: 23000000 INFO @ Tue, 30 Jun 2020 00:54:02: 19000000 INFO @ Tue, 30 Jun 2020 00:54:07: 24000000 INFO @ Tue, 30 Jun 2020 00:54:09: 20000000 INFO @ Tue, 30 Jun 2020 00:54:09: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:54:09: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:54:09: #1 total tags in treatment: 24267011 INFO @ Tue, 30 Jun 2020 00:54:09: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:54:09: #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 00:54:10: #1 tags after filtering in treatment: 24267011 INFO @ Tue, 30 Jun 2020 00:54:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:54:10: #1 finished! INFO @ Tue, 30 Jun 2020 00:54:10: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:54:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:54:11: #2 number of paired peaks: 113 WARNING @ Tue, 30 Jun 2020 00:54:11: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Tue, 30 Jun 2020 00:54:11: start model_add_line... INFO @ Tue, 30 Jun 2020 00:54:11: start X-correlation... INFO @ Tue, 30 Jun 2020 00:54:11: end of X-cor INFO @ Tue, 30 Jun 2020 00:54:11: #2 finished! INFO @ Tue, 30 Jun 2020 00:54:11: #2 predicted fragment length is 46 bps INFO @ Tue, 30 Jun 2020 00:54:11: #2 alternative fragment length(s) may be 46 bps INFO @ Tue, 30 Jun 2020 00:54:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX969931/SRX969931.10_model.r WARNING @ Tue, 30 Jun 2020 00:54:11: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:54:11: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Tue, 30 Jun 2020 00:54:11: #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 00:54:11: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:54:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:54:15: 21000000 INFO @ Tue, 30 Jun 2020 00:54:22: 22000000 INFO @ Tue, 30 Jun 2020 00:54:28: 23000000 INFO @ Tue, 30 Jun 2020 00:54:34: 24000000 INFO @ Tue, 30 Jun 2020 00:54:35: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:54:35: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:54:35: #1 total tags in treatment: 24267011 INFO @ Tue, 30 Jun 2020 00:54:35: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:54:35: #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 00:54:36: #1 tags after filtering in treatment: 24267011 INFO @ Tue, 30 Jun 2020 00:54:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:54:36: #1 finished! INFO @ Tue, 30 Jun 2020 00:54:36: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:54:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:54:37: #2 number of paired peaks: 113 WARNING @ Tue, 30 Jun 2020 00:54:37: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Tue, 30 Jun 2020 00:54:37: start model_add_line... INFO @ Tue, 30 Jun 2020 00:54:37: start X-correlation... INFO @ Tue, 30 Jun 2020 00:54:37: end of X-cor INFO @ Tue, 30 Jun 2020 00:54:37: #2 finished! INFO @ Tue, 30 Jun 2020 00:54:37: #2 predicted fragment length is 46 bps INFO @ Tue, 30 Jun 2020 00:54:37: #2 alternative fragment length(s) may be 46 bps INFO @ Tue, 30 Jun 2020 00:54:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX969931/SRX969931.20_model.r WARNING @ Tue, 30 Jun 2020 00:54:37: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:54:37: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Tue, 30 Jun 2020 00:54:37: #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 00:54:37: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:54:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:54:37: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 00:54:54: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:54:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX969931/SRX969931.05_peaks.xls INFO @ Tue, 30 Jun 2020 00:54:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX969931/SRX969931.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:54:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX969931/SRX969931.05_summits.bed INFO @ Tue, 30 Jun 2020 00:54:57: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1781 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:55:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX969931/SRX969931.10_peaks.xls INFO @ Tue, 30 Jun 2020 00:55:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX969931/SRX969931.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:55:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX969931/SRX969931.10_summits.bed INFO @ Tue, 30 Jun 2020 00:55:14: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1474 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:55:19: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:55:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX969931/SRX969931.20_peaks.xls INFO @ Tue, 30 Jun 2020 00:55:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX969931/SRX969931.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:55:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX969931/SRX969931.20_summits.bed INFO @ Tue, 30 Jun 2020 00:55:39: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (1109 records, 4 fields): 3 millis CompletedMACS2peakCalling