Job ID = 6458280 SRX = SRX5011041 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:23:19 prefetch.2.10.7: 1) Downloading 'SRR8191490'... 2020-06-21T12:23:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:26:21 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:26:21 prefetch.2.10.7: 1) 'SRR8191490' was downloaded successfully 2020-06-21T12:26:21 prefetch.2.10.7: 'SRR8191490' has 0 unresolved dependencies Read 39285389 spots for SRR8191490/SRR8191490.sra Written 39285389 spots for SRR8191490/SRR8191490.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: 00:12:16 39285389 reads; of these: 39285389 (100.00%) were unpaired; of these: 987494 (2.51%) aligned 0 times 26506410 (67.47%) aligned exactly 1 time 11791485 (30.01%) aligned >1 times 97.49% overall alignment rate Time searching: 00:12:16 Overall time: 00:12:16 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 16 files... [bam_rmdupse_core] 15283957 / 38297895 = 0.3991 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 21:48:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011041/SRX5011041.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011041/SRX5011041.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011041/SRX5011041.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011041/SRX5011041.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 21:48:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:48:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:48:51: 1000000 INFO @ Sun, 21 Jun 2020 21:48:56: 2000000 INFO @ Sun, 21 Jun 2020 21:49:01: 3000000 INFO @ Sun, 21 Jun 2020 21:49:06: 4000000 INFO @ Sun, 21 Jun 2020 21:49:11: 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 @ Sun, 21 Jun 2020 21:49:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011041/SRX5011041.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011041/SRX5011041.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011041/SRX5011041.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011041/SRX5011041.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 21:49:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:49:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:49:16: 6000000 INFO @ Sun, 21 Jun 2020 21:49:21: 7000000 INFO @ Sun, 21 Jun 2020 21:49:22: 1000000 INFO @ Sun, 21 Jun 2020 21:49:27: 8000000 INFO @ Sun, 21 Jun 2020 21:49:27: 2000000 INFO @ Sun, 21 Jun 2020 21:49:32: 9000000 INFO @ Sun, 21 Jun 2020 21:49:32: 3000000 INFO @ Sun, 21 Jun 2020 21:49:37: 10000000 INFO @ Sun, 21 Jun 2020 21:49:38: 4000000 INFO @ Sun, 21 Jun 2020 21:49:42: 11000000 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 21:49:43: 5000000 INFO @ Sun, 21 Jun 2020 21:49:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011041/SRX5011041.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011041/SRX5011041.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011041/SRX5011041.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011041/SRX5011041.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 21:49:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:49:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:49:48: 12000000 INFO @ Sun, 21 Jun 2020 21:49:49: 6000000 INFO @ Sun, 21 Jun 2020 21:49:51: 1000000 INFO @ Sun, 21 Jun 2020 21:49:53: 13000000 INFO @ Sun, 21 Jun 2020 21:49:55: 7000000 INFO @ Sun, 21 Jun 2020 21:49:57: 2000000 INFO @ Sun, 21 Jun 2020 21:49:58: 14000000 INFO @ Sun, 21 Jun 2020 21:50:01: 8000000 INFO @ Sun, 21 Jun 2020 21:50:03: 3000000 INFO @ Sun, 21 Jun 2020 21:50:03: 15000000 INFO @ Sun, 21 Jun 2020 21:50:07: 9000000 INFO @ Sun, 21 Jun 2020 21:50:08: 16000000 INFO @ Sun, 21 Jun 2020 21:50:09: 4000000 INFO @ Sun, 21 Jun 2020 21:50:13: 10000000 INFO @ Sun, 21 Jun 2020 21:50:14: 17000000 INFO @ Sun, 21 Jun 2020 21:50:15: 5000000 INFO @ Sun, 21 Jun 2020 21:50:19: 11000000 INFO @ Sun, 21 Jun 2020 21:50:20: 18000000 INFO @ Sun, 21 Jun 2020 21:50:21: 6000000 INFO @ Sun, 21 Jun 2020 21:50:24: 12000000 INFO @ Sun, 21 Jun 2020 21:50:25: 19000000 INFO @ Sun, 21 Jun 2020 21:50:26: 7000000 INFO @ Sun, 21 Jun 2020 21:50:30: 20000000 INFO @ Sun, 21 Jun 2020 21:50:30: 13000000 INFO @ Sun, 21 Jun 2020 21:50:32: 8000000 INFO @ Sun, 21 Jun 2020 21:50:36: 21000000 INFO @ Sun, 21 Jun 2020 21:50:36: 14000000 INFO @ Sun, 21 Jun 2020 21:50:38: 9000000 INFO @ Sun, 21 Jun 2020 21:50:41: 22000000 INFO @ Sun, 21 Jun 2020 21:50:42: 15000000 INFO @ Sun, 21 Jun 2020 21:50:44: 10000000 INFO @ Sun, 21 Jun 2020 21:50:47: 23000000 INFO @ Sun, 21 Jun 2020 21:50:47: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:50:47: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:50:47: #1 total tags in treatment: 23013938 INFO @ Sun, 21 Jun 2020 21:50:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:50:47: #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 21:50:48: #1 tags after filtering in treatment: 23013895 INFO @ Sun, 21 Jun 2020 21:50:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:50:48: #1 finished! INFO @ Sun, 21 Jun 2020 21:50:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:50:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:50:48: 16000000 INFO @ Sun, 21 Jun 2020 21:50:49: 11000000 INFO @ Sun, 21 Jun 2020 21:50:49: #2 number of paired peaks: 1061 INFO @ Sun, 21 Jun 2020 21:50:49: start model_add_line... INFO @ Sun, 21 Jun 2020 21:50:50: start X-correlation... INFO @ Sun, 21 Jun 2020 21:50:50: end of X-cor INFO @ Sun, 21 Jun 2020 21:50:50: #2 finished! INFO @ Sun, 21 Jun 2020 21:50:50: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 21:50:50: #2 alternative fragment length(s) may be 2,47 bps INFO @ Sun, 21 Jun 2020 21:50:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011041/SRX5011041.05_model.r WARNING @ Sun, 21 Jun 2020 21:50:50: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:50:50: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Sun, 21 Jun 2020 21:50:50: #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 21:50:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:50:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:50:54: 17000000 INFO @ Sun, 21 Jun 2020 21:50:55: 12000000 INFO @ Sun, 21 Jun 2020 21:51:00: 13000000 INFO @ Sun, 21 Jun 2020 21:51:00: 18000000 INFO @ Sun, 21 Jun 2020 21:51:06: 14000000 INFO @ Sun, 21 Jun 2020 21:51:06: 19000000 INFO @ Sun, 21 Jun 2020 21:51:11: 15000000 INFO @ Sun, 21 Jun 2020 21:51:12: 20000000 INFO @ Sun, 21 Jun 2020 21:51:17: 16000000 INFO @ Sun, 21 Jun 2020 21:51:18: 21000000 INFO @ Sun, 21 Jun 2020 21:51:23: 17000000 INFO @ Sun, 21 Jun 2020 21:51:24: 22000000 INFO @ Sun, 21 Jun 2020 21:51:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:51:29: 18000000 INFO @ Sun, 21 Jun 2020 21:51:30: 23000000 INFO @ Sun, 21 Jun 2020 21:51:30: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:51:30: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:51:30: #1 total tags in treatment: 23013938 INFO @ Sun, 21 Jun 2020 21:51:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:51:30: #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 21:51:31: #1 tags after filtering in treatment: 23013895 INFO @ Sun, 21 Jun 2020 21:51:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:51:31: #1 finished! INFO @ Sun, 21 Jun 2020 21:51:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:51:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:51:33: #2 number of paired peaks: 1061 INFO @ Sun, 21 Jun 2020 21:51:33: start model_add_line... INFO @ Sun, 21 Jun 2020 21:51:33: start X-correlation... INFO @ Sun, 21 Jun 2020 21:51:33: end of X-cor INFO @ Sun, 21 Jun 2020 21:51:33: #2 finished! INFO @ Sun, 21 Jun 2020 21:51:33: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 21:51:33: #2 alternative fragment length(s) may be 2,47 bps INFO @ Sun, 21 Jun 2020 21:51:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011041/SRX5011041.10_model.r WARNING @ Sun, 21 Jun 2020 21:51:33: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:51:33: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Sun, 21 Jun 2020 21:51:33: #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 21:51:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:51:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:51:34: 19000000 INFO @ Sun, 21 Jun 2020 21:51:40: 20000000 INFO @ Sun, 21 Jun 2020 21:51:45: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:51:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011041/SRX5011041.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:51:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011041/SRX5011041.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:51:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011041/SRX5011041.05_summits.bed INFO @ Sun, 21 Jun 2020 21:51:49: Done! pass1 - making usageList (794 chroms): 2 millis pass2 - checking and writing primary data (4477 records, 4 fields): 65 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:51:50: 22000000 INFO @ Sun, 21 Jun 2020 21:51:55: 23000000 INFO @ Sun, 21 Jun 2020 21:51:56: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:51:56: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:51:56: #1 total tags in treatment: 23013938 INFO @ Sun, 21 Jun 2020 21:51:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:51:56: #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 21:51:57: #1 tags after filtering in treatment: 23013895 INFO @ Sun, 21 Jun 2020 21:51:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:51:57: #1 finished! INFO @ Sun, 21 Jun 2020 21:51:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:51:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:51:58: #2 number of paired peaks: 1061 INFO @ Sun, 21 Jun 2020 21:51:58: start model_add_line... INFO @ Sun, 21 Jun 2020 21:51:58: start X-correlation... INFO @ Sun, 21 Jun 2020 21:51:58: end of X-cor INFO @ Sun, 21 Jun 2020 21:51:58: #2 finished! INFO @ Sun, 21 Jun 2020 21:51:58: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 21:51:58: #2 alternative fragment length(s) may be 2,47 bps INFO @ Sun, 21 Jun 2020 21:51:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011041/SRX5011041.20_model.r WARNING @ Sun, 21 Jun 2020 21:51:58: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:51:58: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Sun, 21 Jun 2020 21:51:58: #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 21:51:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:51:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:52:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:52:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011041/SRX5011041.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:52:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011041/SRX5011041.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:52:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011041/SRX5011041.10_summits.bed INFO @ Sun, 21 Jun 2020 21:52:31: Done! pass1 - making usageList (698 chroms): 2 millis pass2 - checking and writing primary data (3064 records, 4 fields): 41 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:52:36: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:52:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011041/SRX5011041.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:52:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011041/SRX5011041.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:52:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011041/SRX5011041.20_summits.bed INFO @ Sun, 21 Jun 2020 21:52:56: Done! pass1 - making usageList (457 chroms): 1 millis pass2 - checking and writing primary data (1271 records, 4 fields): 26 millis CompletedMACS2peakCalling