Job ID = 6528031 SRX = SRX3981639 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T14:20:35 prefetch.2.10.7: 1) Downloading 'SRR7050301'... 2020-06-29T14:20:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:21:53 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:21:54 prefetch.2.10.7: 'SRR7050301' is valid 2020-06-29T14:21:54 prefetch.2.10.7: 1) 'SRR7050301' was downloaded successfully 2020-06-29T14:21:54 prefetch.2.10.7: 'SRR7050301' has 0 unresolved dependencies Read 14784791 spots for SRR7050301/SRR7050301.sra Written 14784791 spots for SRR7050301/SRR7050301.sra 2020-06-29T14:22:48 prefetch.2.10.7: 1) Downloading 'SRR7050302'... 2020-06-29T14:22:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:24:01 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:24:01 prefetch.2.10.7: 'SRR7050302' is valid 2020-06-29T14:24:01 prefetch.2.10.7: 1) 'SRR7050302' was downloaded successfully 2020-06-29T14:24:02 prefetch.2.10.7: 'SRR7050302' has 0 unresolved dependencies Read 14680451 spots for SRR7050302/SRR7050302.sra Written 14680451 spots for SRR7050302/SRR7050302.sra 2020-06-29T14:25:00 prefetch.2.10.7: 1) Downloading 'SRR7050303'... 2020-06-29T14:25:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:26:21 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:26:21 prefetch.2.10.7: 'SRR7050303' is valid 2020-06-29T14:26:21 prefetch.2.10.7: 1) 'SRR7050303' was downloaded successfully 2020-06-29T14:26:21 prefetch.2.10.7: 'SRR7050303' has 0 unresolved dependencies Read 14663753 spots for SRR7050303/SRR7050303.sra Written 14663753 spots for SRR7050303/SRR7050303.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:10:36 44128995 reads; of these: 44128995 (100.00%) were unpaired; of these: 1756369 (3.98%) aligned 0 times 36290570 (82.24%) aligned exactly 1 time 6082056 (13.78%) aligned >1 times 96.02% overall alignment rate Time searching: 00:10:37 Overall time: 00:10:37 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 20 files... [bam_rmdupse_core] 10887340 / 42372626 = 0.2569 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 @ Mon, 29 Jun 2020 23:56:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981639/SRX3981639.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981639/SRX3981639.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981639/SRX3981639.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981639/SRX3981639.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 @ Mon, 29 Jun 2020 23:56:22: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:56:22: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:56:28: 1000000 INFO @ Mon, 29 Jun 2020 23:56:33: 2000000 INFO @ Mon, 29 Jun 2020 23:56:39: 3000000 INFO @ Mon, 29 Jun 2020 23:56:44: 4000000 INFO @ Mon, 29 Jun 2020 23:56:50: 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 @ Mon, 29 Jun 2020 23:56:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981639/SRX3981639.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981639/SRX3981639.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981639/SRX3981639.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981639/SRX3981639.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 @ Mon, 29 Jun 2020 23:56:52: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:56:52: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:56:55: 6000000 INFO @ Mon, 29 Jun 2020 23:56:58: 1000000 INFO @ Mon, 29 Jun 2020 23:57:01: 7000000 INFO @ Mon, 29 Jun 2020 23:57:04: 2000000 INFO @ Mon, 29 Jun 2020 23:57:07: 8000000 INFO @ Mon, 29 Jun 2020 23:57:09: 3000000 INFO @ Mon, 29 Jun 2020 23:57:13: 9000000 INFO @ Mon, 29 Jun 2020 23:57:15: 4000000 INFO @ Mon, 29 Jun 2020 23:57:18: 10000000 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 @ Mon, 29 Jun 2020 23:57:21: 5000000 INFO @ Mon, 29 Jun 2020 23:57:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981639/SRX3981639.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981639/SRX3981639.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981639/SRX3981639.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981639/SRX3981639.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 @ Mon, 29 Jun 2020 23:57:22: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:57:22: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:57:25: 11000000 INFO @ Mon, 29 Jun 2020 23:57:27: 6000000 INFO @ Mon, 29 Jun 2020 23:57:29: 1000000 INFO @ Mon, 29 Jun 2020 23:57:31: 12000000 INFO @ Mon, 29 Jun 2020 23:57:34: 7000000 INFO @ Mon, 29 Jun 2020 23:57:36: 2000000 INFO @ Mon, 29 Jun 2020 23:57:37: 13000000 INFO @ Mon, 29 Jun 2020 23:57:40: 8000000 INFO @ Mon, 29 Jun 2020 23:57:42: 3000000 INFO @ Mon, 29 Jun 2020 23:57:43: 14000000 INFO @ Mon, 29 Jun 2020 23:57:46: 9000000 INFO @ Mon, 29 Jun 2020 23:57:49: 4000000 INFO @ Mon, 29 Jun 2020 23:57:50: 15000000 INFO @ Mon, 29 Jun 2020 23:57:53: 10000000 INFO @ Mon, 29 Jun 2020 23:57:56: 5000000 INFO @ Mon, 29 Jun 2020 23:57:56: 16000000 INFO @ Mon, 29 Jun 2020 23:57:59: 11000000 INFO @ Mon, 29 Jun 2020 23:58:02: 17000000 INFO @ Mon, 29 Jun 2020 23:58:02: 6000000 INFO @ Mon, 29 Jun 2020 23:58:05: 12000000 INFO @ Mon, 29 Jun 2020 23:58:09: 18000000 INFO @ Mon, 29 Jun 2020 23:58:09: 7000000 INFO @ Mon, 29 Jun 2020 23:58:12: 13000000 INFO @ Mon, 29 Jun 2020 23:58:15: 19000000 INFO @ Mon, 29 Jun 2020 23:58:16: 8000000 INFO @ Mon, 29 Jun 2020 23:58:18: 14000000 INFO @ Mon, 29 Jun 2020 23:58:21: 20000000 INFO @ Mon, 29 Jun 2020 23:58:23: 9000000 INFO @ Mon, 29 Jun 2020 23:58:24: 15000000 INFO @ Mon, 29 Jun 2020 23:58:28: 21000000 INFO @ Mon, 29 Jun 2020 23:58:30: 10000000 INFO @ Mon, 29 Jun 2020 23:58:30: 16000000 INFO @ Mon, 29 Jun 2020 23:58:34: 22000000 INFO @ Mon, 29 Jun 2020 23:58:36: 11000000 INFO @ Mon, 29 Jun 2020 23:58:37: 17000000 INFO @ Mon, 29 Jun 2020 23:58:40: 23000000 INFO @ Mon, 29 Jun 2020 23:58:43: 18000000 INFO @ Mon, 29 Jun 2020 23:58:43: 12000000 INFO @ Mon, 29 Jun 2020 23:58:47: 24000000 INFO @ Mon, 29 Jun 2020 23:58:49: 19000000 INFO @ Mon, 29 Jun 2020 23:58:50: 13000000 INFO @ Mon, 29 Jun 2020 23:58:53: 25000000 INFO @ Mon, 29 Jun 2020 23:58:56: 20000000 INFO @ Mon, 29 Jun 2020 23:58:57: 14000000 INFO @ Mon, 29 Jun 2020 23:58:59: 26000000 INFO @ Mon, 29 Jun 2020 23:59:02: 21000000 INFO @ Mon, 29 Jun 2020 23:59:04: 15000000 INFO @ Mon, 29 Jun 2020 23:59:06: 27000000 INFO @ Mon, 29 Jun 2020 23:59:08: 22000000 INFO @ Mon, 29 Jun 2020 23:59:10: 16000000 INFO @ Mon, 29 Jun 2020 23:59:12: 28000000 INFO @ Mon, 29 Jun 2020 23:59:15: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:59:17: 17000000 INFO @ Mon, 29 Jun 2020 23:59:19: 29000000 INFO @ Mon, 29 Jun 2020 23:59:21: 24000000 INFO @ Mon, 29 Jun 2020 23:59:24: 18000000 INFO @ Mon, 29 Jun 2020 23:59:25: 30000000 INFO @ Mon, 29 Jun 2020 23:59:27: 25000000 INFO @ Mon, 29 Jun 2020 23:59:31: 19000000 INFO @ Mon, 29 Jun 2020 23:59:31: 31000000 INFO @ Mon, 29 Jun 2020 23:59:34: 26000000 INFO @ Mon, 29 Jun 2020 23:59:35: #1 tag size is determined as 51 bps INFO @ Mon, 29 Jun 2020 23:59:35: #1 tag size = 51 INFO @ Mon, 29 Jun 2020 23:59:35: #1 total tags in treatment: 31485286 INFO @ Mon, 29 Jun 2020 23:59:35: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:59:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:59:35: #1 tags after filtering in treatment: 31485286 INFO @ Mon, 29 Jun 2020 23:59:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:59:35: #1 finished! INFO @ Mon, 29 Jun 2020 23:59:35: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:59:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:59:37: #2 number of paired peaks: 1847 INFO @ Mon, 29 Jun 2020 23:59:37: start model_add_line... INFO @ Mon, 29 Jun 2020 23:59:37: start X-correlation... INFO @ Mon, 29 Jun 2020 23:59:37: end of X-cor INFO @ Mon, 29 Jun 2020 23:59:37: #2 finished! INFO @ Mon, 29 Jun 2020 23:59:37: #2 predicted fragment length is 2 bps INFO @ Mon, 29 Jun 2020 23:59:37: #2 alternative fragment length(s) may be 2,59,85,104 bps INFO @ Mon, 29 Jun 2020 23:59:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981639/SRX3981639.05_model.r WARNING @ Mon, 29 Jun 2020 23:59:37: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:59:37: #2 You may need to consider one of the other alternative d(s): 2,59,85,104 WARNING @ Mon, 29 Jun 2020 23:59:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:59:37: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:59:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:59:38: 20000000 INFO @ Mon, 29 Jun 2020 23:59:40: 27000000 INFO @ Mon, 29 Jun 2020 23:59:44: 21000000 INFO @ Mon, 29 Jun 2020 23:59:46: 28000000 INFO @ Mon, 29 Jun 2020 23:59:51: 22000000 INFO @ Mon, 29 Jun 2020 23:59:53: 29000000 BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 23:59:58: 23000000 INFO @ Mon, 29 Jun 2020 23:59:59: 30000000 INFO @ Tue, 30 Jun 2020 00:00:05: 24000000 INFO @ Tue, 30 Jun 2020 00:00:05: 31000000 INFO @ Tue, 30 Jun 2020 00:00:08: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 00:00:08: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 00:00:08: #1 total tags in treatment: 31485286 INFO @ Tue, 30 Jun 2020 00:00:08: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:00:08: #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 00:00:09: #1 tags after filtering in treatment: 31485286 INFO @ Tue, 30 Jun 2020 00:00:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:00:09: #1 finished! INFO @ Tue, 30 Jun 2020 00:00:09: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:00:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:00:11: #2 number of paired peaks: 1847 INFO @ Tue, 30 Jun 2020 00:00:11: start model_add_line... INFO @ Tue, 30 Jun 2020 00:00:11: start X-correlation... INFO @ Tue, 30 Jun 2020 00:00:11: end of X-cor INFO @ Tue, 30 Jun 2020 00:00:11: #2 finished! INFO @ Tue, 30 Jun 2020 00:00:11: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 00:00:11: #2 alternative fragment length(s) may be 2,59,85,104 bps INFO @ Tue, 30 Jun 2020 00:00:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981639/SRX3981639.10_model.r WARNING @ Tue, 30 Jun 2020 00:00:11: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:00:11: #2 You may need to consider one of the other alternative d(s): 2,59,85,104 WARNING @ Tue, 30 Jun 2020 00:00:11: #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 00:00:11: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:00:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:00:11: 25000000 INFO @ Tue, 30 Jun 2020 00:00:16: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:00:18: 26000000 INFO @ Tue, 30 Jun 2020 00:00:24: 27000000 INFO @ Tue, 30 Jun 2020 00:00:30: 28000000 INFO @ Tue, 30 Jun 2020 00:00:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981639/SRX3981639.05_peaks.xls INFO @ Tue, 30 Jun 2020 00:00:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981639/SRX3981639.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:00:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981639/SRX3981639.05_summits.bed INFO @ Tue, 30 Jun 2020 00:00:34: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:00:37: 29000000 INFO @ Tue, 30 Jun 2020 00:00:43: 30000000 INFO @ Tue, 30 Jun 2020 00:00:49: 31000000 INFO @ Tue, 30 Jun 2020 00:00:52: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:00:52: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 00:00:52: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 00:00:52: #1 total tags in treatment: 31485286 INFO @ Tue, 30 Jun 2020 00:00:52: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:00:52: #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 00:00:53: #1 tags after filtering in treatment: 31485286 INFO @ Tue, 30 Jun 2020 00:00:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:00:53: #1 finished! INFO @ Tue, 30 Jun 2020 00:00:53: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:00:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:00:55: #2 number of paired peaks: 1847 INFO @ Tue, 30 Jun 2020 00:00:55: start model_add_line... INFO @ Tue, 30 Jun 2020 00:00:55: start X-correlation... INFO @ Tue, 30 Jun 2020 00:00:55: end of X-cor INFO @ Tue, 30 Jun 2020 00:00:55: #2 finished! INFO @ Tue, 30 Jun 2020 00:00:55: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 00:00:55: #2 alternative fragment length(s) may be 2,59,85,104 bps INFO @ Tue, 30 Jun 2020 00:00:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981639/SRX3981639.20_model.r WARNING @ Tue, 30 Jun 2020 00:00:55: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:00:55: #2 You may need to consider one of the other alternative d(s): 2,59,85,104 WARNING @ Tue, 30 Jun 2020 00:00:55: #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 00:00:55: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:00:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:01:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981639/SRX3981639.10_peaks.xls INFO @ Tue, 30 Jun 2020 00:01:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981639/SRX3981639.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:01:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981639/SRX3981639.10_summits.bed INFO @ Tue, 30 Jun 2020 00:01:10: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:01:35: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:01:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981639/SRX3981639.20_peaks.xls INFO @ Tue, 30 Jun 2020 00:01:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981639/SRX3981639.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:01:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981639/SRX3981639.20_summits.bed INFO @ Tue, 30 Jun 2020 00:01:53: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling