Job ID = 6456130 SRX = SRX318809 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:33:04 prefetch.2.10.7: 1) Downloading 'SRR927154'... 2020-06-21T10:33:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:42:16 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:42:16 prefetch.2.10.7: 1) 'SRR927154' was downloaded successfully Read 34282290 spots for SRR927154/SRR927154.sra Written 34282290 spots for SRR927154/SRR927154.sra 2020-06-21T10:44:00 prefetch.2.10.7: 1) Downloading 'SRR927155'... 2020-06-21T10:44:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:51:50 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:51:50 prefetch.2.10.7: 1) 'SRR927155' was downloaded successfully Read 40789239 spots for SRR927155/SRR927155.sra Written 40789239 spots for SRR927155/SRR927155.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: 00:25:37 75071529 reads; of these: 75071529 (100.00%) were unpaired; of these: 2190491 (2.92%) aligned 0 times 26389911 (35.15%) aligned exactly 1 time 46491127 (61.93%) aligned >1 times 97.08% overall alignment rate Time searching: 00:25:37 Overall time: 00:25:37 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 32 files... [bam_rmdupse_core] 32114705 / 72881038 = 0.4406 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 20:35:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX318809/SRX318809.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX318809/SRX318809.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX318809/SRX318809.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX318809/SRX318809.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 20:35:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:35:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:35:59: 1000000 INFO @ Sun, 21 Jun 2020 20:36:07: 2000000 INFO @ Sun, 21 Jun 2020 20:36:15: 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 20:36:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX318809/SRX318809.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX318809/SRX318809.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX318809/SRX318809.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX318809/SRX318809.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 20:36:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:36:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:36:23: 4000000 INFO @ Sun, 21 Jun 2020 20:36:31: 1000000 INFO @ Sun, 21 Jun 2020 20:36:32: 5000000 INFO @ Sun, 21 Jun 2020 20:36:39: 2000000 INFO @ Sun, 21 Jun 2020 20:36:40: 6000000 INFO @ Sun, 21 Jun 2020 20:36:48: 3000000 INFO @ Sun, 21 Jun 2020 20:36:49: 7000000 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 20:36:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX318809/SRX318809.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX318809/SRX318809.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX318809/SRX318809.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX318809/SRX318809.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 20:36:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:36:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:36:56: 4000000 INFO @ Sun, 21 Jun 2020 20:36:58: 8000000 INFO @ Sun, 21 Jun 2020 20:37:00: 1000000 INFO @ Sun, 21 Jun 2020 20:37:05: 5000000 INFO @ Sun, 21 Jun 2020 20:37:06: 9000000 INFO @ Sun, 21 Jun 2020 20:37:08: 2000000 INFO @ Sun, 21 Jun 2020 20:37:13: 6000000 INFO @ Sun, 21 Jun 2020 20:37:15: 10000000 INFO @ Sun, 21 Jun 2020 20:37:17: 3000000 INFO @ Sun, 21 Jun 2020 20:37:22: 7000000 INFO @ Sun, 21 Jun 2020 20:37:24: 11000000 INFO @ Sun, 21 Jun 2020 20:37:25: 4000000 INFO @ Sun, 21 Jun 2020 20:37:31: 8000000 INFO @ Sun, 21 Jun 2020 20:37:33: 12000000 INFO @ Sun, 21 Jun 2020 20:37:33: 5000000 INFO @ Sun, 21 Jun 2020 20:37:39: 9000000 INFO @ Sun, 21 Jun 2020 20:37:41: 6000000 INFO @ Sun, 21 Jun 2020 20:37:41: 13000000 INFO @ Sun, 21 Jun 2020 20:37:48: 10000000 INFO @ Sun, 21 Jun 2020 20:37:49: 7000000 INFO @ Sun, 21 Jun 2020 20:37:50: 14000000 INFO @ Sun, 21 Jun 2020 20:37:57: 11000000 INFO @ Sun, 21 Jun 2020 20:37:57: 8000000 INFO @ Sun, 21 Jun 2020 20:37:59: 15000000 INFO @ Sun, 21 Jun 2020 20:38:05: 9000000 INFO @ Sun, 21 Jun 2020 20:38:05: 12000000 INFO @ Sun, 21 Jun 2020 20:38:07: 16000000 INFO @ Sun, 21 Jun 2020 20:38:13: 10000000 INFO @ Sun, 21 Jun 2020 20:38:14: 13000000 INFO @ Sun, 21 Jun 2020 20:38:16: 17000000 INFO @ Sun, 21 Jun 2020 20:38:20: 11000000 INFO @ Sun, 21 Jun 2020 20:38:23: 14000000 INFO @ Sun, 21 Jun 2020 20:38:25: 18000000 INFO @ Sun, 21 Jun 2020 20:38:28: 12000000 INFO @ Sun, 21 Jun 2020 20:38:32: 15000000 INFO @ Sun, 21 Jun 2020 20:38:35: 19000000 INFO @ Sun, 21 Jun 2020 20:38:36: 13000000 INFO @ Sun, 21 Jun 2020 20:38:42: 16000000 INFO @ Sun, 21 Jun 2020 20:38:43: 14000000 INFO @ Sun, 21 Jun 2020 20:38:45: 20000000 INFO @ Sun, 21 Jun 2020 20:38:51: 15000000 INFO @ Sun, 21 Jun 2020 20:38:51: 17000000 INFO @ Sun, 21 Jun 2020 20:38:54: 21000000 INFO @ Sun, 21 Jun 2020 20:38:58: 16000000 INFO @ Sun, 21 Jun 2020 20:39:00: 18000000 INFO @ Sun, 21 Jun 2020 20:39:04: 22000000 INFO @ Sun, 21 Jun 2020 20:39:06: 17000000 INFO @ Sun, 21 Jun 2020 20:39:10: 19000000 INFO @ Sun, 21 Jun 2020 20:39:13: 23000000 INFO @ Sun, 21 Jun 2020 20:39:13: 18000000 INFO @ Sun, 21 Jun 2020 20:39:19: 20000000 INFO @ Sun, 21 Jun 2020 20:39:21: 19000000 INFO @ Sun, 21 Jun 2020 20:39:23: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:39:28: 20000000 INFO @ Sun, 21 Jun 2020 20:39:29: 21000000 INFO @ Sun, 21 Jun 2020 20:39:32: 25000000 INFO @ Sun, 21 Jun 2020 20:39:36: 21000000 INFO @ Sun, 21 Jun 2020 20:39:38: 22000000 INFO @ Sun, 21 Jun 2020 20:39:41: 26000000 INFO @ Sun, 21 Jun 2020 20:39:43: 22000000 INFO @ Sun, 21 Jun 2020 20:39:48: 23000000 INFO @ Sun, 21 Jun 2020 20:39:51: 27000000 INFO @ Sun, 21 Jun 2020 20:39:51: 23000000 INFO @ Sun, 21 Jun 2020 20:39:57: 24000000 INFO @ Sun, 21 Jun 2020 20:39:58: 24000000 INFO @ Sun, 21 Jun 2020 20:40:00: 28000000 INFO @ Sun, 21 Jun 2020 20:40:06: 25000000 INFO @ Sun, 21 Jun 2020 20:40:07: 25000000 INFO @ Sun, 21 Jun 2020 20:40:09: 29000000 INFO @ Sun, 21 Jun 2020 20:40:15: 26000000 INFO @ Sun, 21 Jun 2020 20:40:15: 26000000 INFO @ Sun, 21 Jun 2020 20:40:17: 30000000 INFO @ Sun, 21 Jun 2020 20:40:24: 27000000 INFO @ Sun, 21 Jun 2020 20:40:24: 27000000 INFO @ Sun, 21 Jun 2020 20:40:26: 31000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:40:33: 28000000 INFO @ Sun, 21 Jun 2020 20:40:33: 28000000 INFO @ Sun, 21 Jun 2020 20:40:35: 32000000 INFO @ Sun, 21 Jun 2020 20:40:42: 29000000 INFO @ Sun, 21 Jun 2020 20:40:42: 29000000 INFO @ Sun, 21 Jun 2020 20:40:44: 33000000 INFO @ Sun, 21 Jun 2020 20:40:51: 30000000 INFO @ Sun, 21 Jun 2020 20:40:51: 30000000 INFO @ Sun, 21 Jun 2020 20:40:53: 34000000 INFO @ Sun, 21 Jun 2020 20:41:00: 31000000 INFO @ Sun, 21 Jun 2020 20:41:01: 31000000 INFO @ Sun, 21 Jun 2020 20:41:01: 35000000 INFO @ Sun, 21 Jun 2020 20:41:10: 36000000 INFO @ Sun, 21 Jun 2020 20:41:10: 32000000 INFO @ Sun, 21 Jun 2020 20:41:10: 32000000 INFO @ Sun, 21 Jun 2020 20:41:18: 37000000 INFO @ Sun, 21 Jun 2020 20:41:20: 33000000 INFO @ Sun, 21 Jun 2020 20:41:20: 33000000 INFO @ Sun, 21 Jun 2020 20:41:26: 38000000 INFO @ Sun, 21 Jun 2020 20:41:28: 34000000 INFO @ Sun, 21 Jun 2020 20:41:29: 34000000 INFO @ Sun, 21 Jun 2020 20:41:35: 39000000 INFO @ Sun, 21 Jun 2020 20:41:37: 35000000 INFO @ Sun, 21 Jun 2020 20:41:37: 35000000 INFO @ Sun, 21 Jun 2020 20:41:43: 40000000 INFO @ Sun, 21 Jun 2020 20:41:44: 36000000 INFO @ Sun, 21 Jun 2020 20:41:45: 36000000 INFO @ Sun, 21 Jun 2020 20:41:49: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:41:49: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:41:49: #1 total tags in treatment: 40766333 INFO @ Sun, 21 Jun 2020 20:41:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:41:49: #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 20:41:50: #1 tags after filtering in treatment: 40766316 INFO @ Sun, 21 Jun 2020 20:41:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:41:50: #1 finished! INFO @ Sun, 21 Jun 2020 20:41:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:41:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:41:52: 37000000 INFO @ Sun, 21 Jun 2020 20:41:53: #2 number of paired peaks: 1432 INFO @ Sun, 21 Jun 2020 20:41:53: start model_add_line... INFO @ Sun, 21 Jun 2020 20:41:53: 37000000 INFO @ Sun, 21 Jun 2020 20:41:53: start X-correlation... INFO @ Sun, 21 Jun 2020 20:41:53: end of X-cor INFO @ Sun, 21 Jun 2020 20:41:53: #2 finished! INFO @ Sun, 21 Jun 2020 20:41:53: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 20:41:53: #2 alternative fragment length(s) may be 1,40 bps INFO @ Sun, 21 Jun 2020 20:41:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX318809/SRX318809.05_model.r WARNING @ Sun, 21 Jun 2020 20:41:53: #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 20:41:53: #2 You may need to consider one of the other alternative d(s): 1,40 WARNING @ Sun, 21 Jun 2020 20:41:53: #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 20:41:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:41:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:41:59: 38000000 INFO @ Sun, 21 Jun 2020 20:42:01: 38000000 INFO @ Sun, 21 Jun 2020 20:42:06: 39000000 INFO @ Sun, 21 Jun 2020 20:42:09: 39000000 INFO @ Sun, 21 Jun 2020 20:42:14: 40000000 INFO @ Sun, 21 Jun 2020 20:42:17: 40000000 INFO @ Sun, 21 Jun 2020 20:42:20: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:42:20: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:42:20: #1 total tags in treatment: 40766333 INFO @ Sun, 21 Jun 2020 20:42:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:42:20: #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 20:42:21: #1 tags after filtering in treatment: 40766316 INFO @ Sun, 21 Jun 2020 20:42:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:42:21: #1 finished! INFO @ Sun, 21 Jun 2020 20:42:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:42:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:42:23: #2 number of paired peaks: 1432 INFO @ Sun, 21 Jun 2020 20:42:23: start model_add_line... INFO @ Sun, 21 Jun 2020 20:42:23: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:42:23: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:42:23: #1 total tags in treatment: 40766333 INFO @ Sun, 21 Jun 2020 20:42:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:42:23: #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 20:42:24: start X-correlation... INFO @ Sun, 21 Jun 2020 20:42:24: end of X-cor INFO @ Sun, 21 Jun 2020 20:42:24: #2 finished! INFO @ Sun, 21 Jun 2020 20:42:24: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 20:42:24: #2 alternative fragment length(s) may be 1,40 bps INFO @ Sun, 21 Jun 2020 20:42:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX318809/SRX318809.20_model.r WARNING @ Sun, 21 Jun 2020 20:42:24: #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 20:42:24: #2 You may need to consider one of the other alternative d(s): 1,40 WARNING @ Sun, 21 Jun 2020 20:42:24: #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 20:42:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:42:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:42:24: #1 tags after filtering in treatment: 40766316 INFO @ Sun, 21 Jun 2020 20:42:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:42:24: #1 finished! INFO @ Sun, 21 Jun 2020 20:42:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:42:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:42:27: #2 number of paired peaks: 1432 INFO @ Sun, 21 Jun 2020 20:42:27: start model_add_line... INFO @ Sun, 21 Jun 2020 20:42:27: start X-correlation... INFO @ Sun, 21 Jun 2020 20:42:27: end of X-cor INFO @ Sun, 21 Jun 2020 20:42:27: #2 finished! INFO @ Sun, 21 Jun 2020 20:42:27: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 20:42:27: #2 alternative fragment length(s) may be 1,40 bps INFO @ Sun, 21 Jun 2020 20:42:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX318809/SRX318809.10_model.r WARNING @ Sun, 21 Jun 2020 20:42:27: #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 20:42:27: #2 You may need to consider one of the other alternative d(s): 1,40 WARNING @ Sun, 21 Jun 2020 20:42:27: #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 20:42:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:42:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:42:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:43:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX318809/SRX318809.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:43:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX318809/SRX318809.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:43:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX318809/SRX318809.05_summits.bed INFO @ Sun, 21 Jun 2020 20:43:02: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:43:09: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:43:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:43:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX318809/SRX318809.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:43:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX318809/SRX318809.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:43:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX318809/SRX318809.20_summits.bed INFO @ Sun, 21 Jun 2020 20:43:29: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:43:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX318809/SRX318809.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:43:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX318809/SRX318809.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:43:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX318809/SRX318809.10_summits.bed INFO @ Sun, 21 Jun 2020 20:43:35: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling