Job ID = 6458760 SRX = SRX5436037 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:51:55 prefetch.2.10.7: 1) Downloading 'SRR8637369'... 2020-06-21T12:51:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:56:57 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:56:57 prefetch.2.10.7: 1) 'SRR8637369' was downloaded successfully Read 36117836 spots for SRR8637369/SRR8637369.sra Written 36117836 spots for SRR8637369/SRR8637369.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: 00:11:14 36117836 reads; of these: 36117836 (100.00%) were unpaired; of these: 1535221 (4.25%) aligned 0 times 23602891 (65.35%) aligned exactly 1 time 10979724 (30.40%) aligned >1 times 95.75% overall alignment rate Time searching: 00:11:14 Overall time: 00:11:14 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] 6733424 / 34582615 = 0.1947 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 22:19:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5436037/SRX5436037.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5436037/SRX5436037.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5436037/SRX5436037.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5436037/SRX5436037.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 22:19:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:19:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:19:28: 1000000 INFO @ Sun, 21 Jun 2020 22:19:35: 2000000 INFO @ Sun, 21 Jun 2020 22:19:42: 3000000 INFO @ Sun, 21 Jun 2020 22:19:48: 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 @ Sun, 21 Jun 2020 22:19:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5436037/SRX5436037.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5436037/SRX5436037.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5436037/SRX5436037.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5436037/SRX5436037.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 22:19:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:19:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:19:55: 5000000 INFO @ Sun, 21 Jun 2020 22:20:00: 1000000 INFO @ Sun, 21 Jun 2020 22:20:02: 6000000 INFO @ Sun, 21 Jun 2020 22:20:08: 2000000 INFO @ Sun, 21 Jun 2020 22:20:09: 7000000 INFO @ Sun, 21 Jun 2020 22:20:16: 8000000 INFO @ Sun, 21 Jun 2020 22:20:17: 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 @ Sun, 21 Jun 2020 22:20:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5436037/SRX5436037.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5436037/SRX5436037.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5436037/SRX5436037.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5436037/SRX5436037.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 22:20:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:20:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:20:23: 9000000 INFO @ Sun, 21 Jun 2020 22:20:26: 4000000 INFO @ Sun, 21 Jun 2020 22:20:29: 1000000 INFO @ Sun, 21 Jun 2020 22:20:31: 10000000 INFO @ Sun, 21 Jun 2020 22:20:34: 5000000 INFO @ Sun, 21 Jun 2020 22:20:36: 2000000 INFO @ Sun, 21 Jun 2020 22:20:39: 11000000 INFO @ Sun, 21 Jun 2020 22:20:43: 6000000 INFO @ Sun, 21 Jun 2020 22:20:44: 3000000 INFO @ Sun, 21 Jun 2020 22:20:47: 12000000 INFO @ Sun, 21 Jun 2020 22:20:51: 7000000 INFO @ Sun, 21 Jun 2020 22:20:52: 4000000 INFO @ Sun, 21 Jun 2020 22:20:55: 13000000 INFO @ Sun, 21 Jun 2020 22:20:59: 5000000 INFO @ Sun, 21 Jun 2020 22:21:00: 8000000 INFO @ Sun, 21 Jun 2020 22:21:02: 14000000 INFO @ Sun, 21 Jun 2020 22:21:07: 6000000 INFO @ Sun, 21 Jun 2020 22:21:08: 9000000 INFO @ Sun, 21 Jun 2020 22:21:10: 15000000 INFO @ Sun, 21 Jun 2020 22:21:14: 7000000 INFO @ Sun, 21 Jun 2020 22:21:17: 10000000 INFO @ Sun, 21 Jun 2020 22:21:18: 16000000 INFO @ Sun, 21 Jun 2020 22:21:22: 8000000 INFO @ Sun, 21 Jun 2020 22:21:25: 17000000 INFO @ Sun, 21 Jun 2020 22:21:26: 11000000 INFO @ Sun, 21 Jun 2020 22:21:30: 9000000 INFO @ Sun, 21 Jun 2020 22:21:33: 18000000 INFO @ Sun, 21 Jun 2020 22:21:34: 12000000 INFO @ Sun, 21 Jun 2020 22:21:37: 10000000 INFO @ Sun, 21 Jun 2020 22:21:41: 19000000 INFO @ Sun, 21 Jun 2020 22:21:43: 13000000 INFO @ Sun, 21 Jun 2020 22:21:45: 11000000 INFO @ Sun, 21 Jun 2020 22:21:48: 20000000 INFO @ Sun, 21 Jun 2020 22:21:51: 14000000 INFO @ Sun, 21 Jun 2020 22:21:52: 12000000 INFO @ Sun, 21 Jun 2020 22:21:56: 21000000 INFO @ Sun, 21 Jun 2020 22:22:00: 15000000 INFO @ Sun, 21 Jun 2020 22:22:00: 13000000 INFO @ Sun, 21 Jun 2020 22:22:04: 22000000 INFO @ Sun, 21 Jun 2020 22:22:08: 14000000 INFO @ Sun, 21 Jun 2020 22:22:08: 16000000 INFO @ Sun, 21 Jun 2020 22:22:12: 23000000 INFO @ Sun, 21 Jun 2020 22:22:15: 15000000 INFO @ Sun, 21 Jun 2020 22:22:17: 17000000 INFO @ Sun, 21 Jun 2020 22:22:20: 24000000 INFO @ Sun, 21 Jun 2020 22:22:23: 16000000 INFO @ Sun, 21 Jun 2020 22:22:25: 18000000 INFO @ Sun, 21 Jun 2020 22:22:27: 25000000 INFO @ Sun, 21 Jun 2020 22:22:30: 17000000 INFO @ Sun, 21 Jun 2020 22:22:34: 19000000 INFO @ Sun, 21 Jun 2020 22:22:35: 26000000 INFO @ Sun, 21 Jun 2020 22:22:38: 18000000 INFO @ Sun, 21 Jun 2020 22:22:42: 27000000 INFO @ Sun, 21 Jun 2020 22:22:43: 20000000 INFO @ Sun, 21 Jun 2020 22:22:45: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:22:49: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:22:49: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:22:49: #1 total tags in treatment: 27849191 INFO @ Sun, 21 Jun 2020 22:22:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:22:49: #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 22:22:50: #1 tags after filtering in treatment: 27849143 INFO @ Sun, 21 Jun 2020 22:22:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:22:50: #1 finished! INFO @ Sun, 21 Jun 2020 22:22:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:22:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:22:52: 21000000 INFO @ Sun, 21 Jun 2020 22:22:52: #2 number of paired peaks: 1124 INFO @ Sun, 21 Jun 2020 22:22:52: start model_add_line... INFO @ Sun, 21 Jun 2020 22:22:53: start X-correlation... INFO @ Sun, 21 Jun 2020 22:22:53: end of X-cor INFO @ Sun, 21 Jun 2020 22:22:53: #2 finished! INFO @ Sun, 21 Jun 2020 22:22:53: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 22:22:53: #2 alternative fragment length(s) may be 1,28 bps INFO @ Sun, 21 Jun 2020 22:22:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5436037/SRX5436037.05_model.r WARNING @ Sun, 21 Jun 2020 22:22:53: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:22:53: #2 You may need to consider one of the other alternative d(s): 1,28 WARNING @ Sun, 21 Jun 2020 22:22:53: #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 22:22:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:22:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:22:53: 20000000 INFO @ Sun, 21 Jun 2020 22:23:00: 21000000 INFO @ Sun, 21 Jun 2020 22:23:01: 22000000 INFO @ Sun, 21 Jun 2020 22:23:08: 22000000 INFO @ Sun, 21 Jun 2020 22:23:10: 23000000 INFO @ Sun, 21 Jun 2020 22:23:16: 23000000 INFO @ Sun, 21 Jun 2020 22:23:20: 24000000 INFO @ Sun, 21 Jun 2020 22:23:24: 24000000 INFO @ Sun, 21 Jun 2020 22:23:29: 25000000 INFO @ Sun, 21 Jun 2020 22:23:32: 25000000 INFO @ Sun, 21 Jun 2020 22:23:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:23:38: 26000000 INFO @ Sun, 21 Jun 2020 22:23:40: 26000000 INFO @ Sun, 21 Jun 2020 22:23:47: 27000000 INFO @ Sun, 21 Jun 2020 22:23:49: 27000000 INFO @ Sun, 21 Jun 2020 22:23:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5436037/SRX5436037.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:23:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5436037/SRX5436037.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:23:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5436037/SRX5436037.05_summits.bed INFO @ Sun, 21 Jun 2020 22:23:52: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:23:55: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:23:55: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:23:55: #1 total tags in treatment: 27849191 INFO @ Sun, 21 Jun 2020 22:23:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:23:55: #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 22:23:56: #1 tags after filtering in treatment: 27849143 INFO @ Sun, 21 Jun 2020 22:23:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:23:56: #1 finished! INFO @ Sun, 21 Jun 2020 22:23:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:23:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:23:56: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:23:56: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:23:56: #1 total tags in treatment: 27849191 INFO @ Sun, 21 Jun 2020 22:23:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:23:56: #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 22:23:57: #1 tags after filtering in treatment: 27849143 INFO @ Sun, 21 Jun 2020 22:23:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:23:57: #1 finished! INFO @ Sun, 21 Jun 2020 22:23:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:23:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:23:58: #2 number of paired peaks: 1124 INFO @ Sun, 21 Jun 2020 22:23:58: start model_add_line... INFO @ Sun, 21 Jun 2020 22:23:58: start X-correlation... INFO @ Sun, 21 Jun 2020 22:23:58: end of X-cor INFO @ Sun, 21 Jun 2020 22:23:58: #2 finished! INFO @ Sun, 21 Jun 2020 22:23:58: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 22:23:58: #2 alternative fragment length(s) may be 1,28 bps INFO @ Sun, 21 Jun 2020 22:23:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5436037/SRX5436037.10_model.r WARNING @ Sun, 21 Jun 2020 22:23:58: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:23:58: #2 You may need to consider one of the other alternative d(s): 1,28 WARNING @ Sun, 21 Jun 2020 22:23:58: #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 22:23:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:23:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:23:59: #2 number of paired peaks: 1124 INFO @ Sun, 21 Jun 2020 22:23:59: start model_add_line... INFO @ Sun, 21 Jun 2020 22:23:59: start X-correlation... INFO @ Sun, 21 Jun 2020 22:23:59: end of X-cor INFO @ Sun, 21 Jun 2020 22:23:59: #2 finished! INFO @ Sun, 21 Jun 2020 22:23:59: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 22:23:59: #2 alternative fragment length(s) may be 1,28 bps INFO @ Sun, 21 Jun 2020 22:23:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5436037/SRX5436037.20_model.r WARNING @ Sun, 21 Jun 2020 22:23:59: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:23:59: #2 You may need to consider one of the other alternative d(s): 1,28 WARNING @ Sun, 21 Jun 2020 22:23:59: #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 22:23:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:23:59: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:24:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:24:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:24:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5436037/SRX5436037.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:24:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5436037/SRX5436037.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:24:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5436037/SRX5436037.10_summits.bed INFO @ Sun, 21 Jun 2020 22:24:58: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:25:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5436037/SRX5436037.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:25:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5436037/SRX5436037.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:25:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5436037/SRX5436037.20_summits.bed INFO @ Sun, 21 Jun 2020 22:25:00: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling