Job ID = 6459900 SRX = SRX969929 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:49:04 prefetch.2.10.7: 1) Downloading 'SRR1931645'... 2020-06-21T13:49:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:52:46 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:52:46 prefetch.2.10.7: 1) 'SRR1931645' was downloaded successfully Read 35931507 spots for SRR1931645/SRR1931645.sra Written 35931507 spots for SRR1931645/SRR1931645.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: 00:10:54 35931507 reads; of these: 35931507 (100.00%) were unpaired; of these: 1198382 (3.34%) aligned 0 times 24476473 (68.12%) aligned exactly 1 time 10256652 (28.55%) aligned >1 times 96.66% overall alignment rate Time searching: 00:10:54 Overall time: 00:10:54 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] 6914666 / 34733125 = 0.1991 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 23:13:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX969929/SRX969929.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX969929/SRX969929.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX969929/SRX969929.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX969929/SRX969929.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 23:13:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 23:13:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 23:13:07: 1000000 INFO @ Sun, 21 Jun 2020 23:13:13: 2000000 INFO @ Sun, 21 Jun 2020 23:13:19: 3000000 INFO @ Sun, 21 Jun 2020 23:13:25: 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 23:13:31: 5000000 INFO @ Sun, 21 Jun 2020 23:13:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX969929/SRX969929.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX969929/SRX969929.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX969929/SRX969929.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX969929/SRX969929.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 23:13:32: #1 read tag files... INFO @ Sun, 21 Jun 2020 23:13:32: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 23:13:37: 6000000 INFO @ Sun, 21 Jun 2020 23:13:37: 1000000 INFO @ Sun, 21 Jun 2020 23:13:43: 7000000 INFO @ Sun, 21 Jun 2020 23:13:43: 2000000 INFO @ Sun, 21 Jun 2020 23:13:49: 3000000 INFO @ Sun, 21 Jun 2020 23:13:49: 8000000 INFO @ Sun, 21 Jun 2020 23:13:55: 4000000 INFO @ Sun, 21 Jun 2020 23:13:55: 9000000 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 23:14:00: 5000000 INFO @ Sun, 21 Jun 2020 23:14:01: 10000000 INFO @ Sun, 21 Jun 2020 23:14:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX969929/SRX969929.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX969929/SRX969929.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX969929/SRX969929.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX969929/SRX969929.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 23:14:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 23:14:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 23:14:06: 6000000 INFO @ Sun, 21 Jun 2020 23:14:08: 11000000 INFO @ Sun, 21 Jun 2020 23:14:08: 1000000 INFO @ Sun, 21 Jun 2020 23:14:12: 7000000 INFO @ Sun, 21 Jun 2020 23:14:14: 12000000 INFO @ Sun, 21 Jun 2020 23:14:14: 2000000 INFO @ Sun, 21 Jun 2020 23:14:18: 8000000 INFO @ Sun, 21 Jun 2020 23:14:20: 13000000 INFO @ Sun, 21 Jun 2020 23:14:20: 3000000 INFO @ Sun, 21 Jun 2020 23:14:23: 9000000 INFO @ Sun, 21 Jun 2020 23:14:26: 14000000 INFO @ Sun, 21 Jun 2020 23:14:27: 4000000 INFO @ Sun, 21 Jun 2020 23:14:29: 10000000 INFO @ Sun, 21 Jun 2020 23:14:32: 15000000 INFO @ Sun, 21 Jun 2020 23:14:33: 5000000 INFO @ Sun, 21 Jun 2020 23:14:35: 11000000 INFO @ Sun, 21 Jun 2020 23:14:38: 16000000 INFO @ Sun, 21 Jun 2020 23:14:39: 6000000 INFO @ Sun, 21 Jun 2020 23:14:41: 12000000 INFO @ Sun, 21 Jun 2020 23:14:45: 17000000 INFO @ Sun, 21 Jun 2020 23:14:46: 7000000 INFO @ Sun, 21 Jun 2020 23:14:46: 13000000 INFO @ Sun, 21 Jun 2020 23:14:51: 18000000 INFO @ Sun, 21 Jun 2020 23:14:52: 14000000 INFO @ Sun, 21 Jun 2020 23:14:52: 8000000 INFO @ Sun, 21 Jun 2020 23:14:57: 19000000 INFO @ Sun, 21 Jun 2020 23:14:58: 15000000 INFO @ Sun, 21 Jun 2020 23:14:58: 9000000 INFO @ Sun, 21 Jun 2020 23:15:03: 20000000 INFO @ Sun, 21 Jun 2020 23:15:04: 16000000 INFO @ Sun, 21 Jun 2020 23:15:05: 10000000 INFO @ Sun, 21 Jun 2020 23:15:09: 17000000 INFO @ Sun, 21 Jun 2020 23:15:09: 21000000 INFO @ Sun, 21 Jun 2020 23:15:11: 11000000 INFO @ Sun, 21 Jun 2020 23:15:15: 18000000 INFO @ Sun, 21 Jun 2020 23:15:16: 22000000 INFO @ Sun, 21 Jun 2020 23:15:18: 12000000 INFO @ Sun, 21 Jun 2020 23:15:21: 19000000 INFO @ Sun, 21 Jun 2020 23:15:22: 23000000 INFO @ Sun, 21 Jun 2020 23:15:24: 13000000 INFO @ Sun, 21 Jun 2020 23:15:26: 20000000 INFO @ Sun, 21 Jun 2020 23:15:28: 24000000 INFO @ Sun, 21 Jun 2020 23:15:31: 14000000 INFO @ Sun, 21 Jun 2020 23:15:32: 21000000 INFO @ Sun, 21 Jun 2020 23:15:35: 25000000 INFO @ Sun, 21 Jun 2020 23:15:37: 15000000 INFO @ Sun, 21 Jun 2020 23:15:38: 22000000 INFO @ Sun, 21 Jun 2020 23:15:41: 26000000 INFO @ Sun, 21 Jun 2020 23:15:43: 16000000 INFO @ Sun, 21 Jun 2020 23:15:44: 23000000 INFO @ Sun, 21 Jun 2020 23:15:47: 27000000 INFO @ Sun, 21 Jun 2020 23:15:49: 24000000 INFO @ Sun, 21 Jun 2020 23:15:50: 17000000 INFO @ Sun, 21 Jun 2020 23:15:52: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 23:15:52: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 23:15:52: #1 total tags in treatment: 27818459 INFO @ Sun, 21 Jun 2020 23:15:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 23:15:52: #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 23:15:53: #1 tags after filtering in treatment: 27818458 INFO @ Sun, 21 Jun 2020 23:15:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 23:15:53: #1 finished! INFO @ Sun, 21 Jun 2020 23:15:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 23:15:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 23:15:55: #2 number of paired peaks: 240 WARNING @ Sun, 21 Jun 2020 23:15:55: Fewer paired peaks (240) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 240 pairs to build model! INFO @ Sun, 21 Jun 2020 23:15:55: start model_add_line... INFO @ Sun, 21 Jun 2020 23:15:55: start X-correlation... INFO @ Sun, 21 Jun 2020 23:15:55: end of X-cor INFO @ Sun, 21 Jun 2020 23:15:55: #2 finished! INFO @ Sun, 21 Jun 2020 23:15:55: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 23:15:55: #2 alternative fragment length(s) may be 1,12,19,38,557 bps INFO @ Sun, 21 Jun 2020 23:15:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX969929/SRX969929.05_model.r WARNING @ Sun, 21 Jun 2020 23:15:55: #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 23:15:55: #2 You may need to consider one of the other alternative d(s): 1,12,19,38,557 WARNING @ Sun, 21 Jun 2020 23:15:55: #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 23:15:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 23:15:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 23:15:55: 25000000 INFO @ Sun, 21 Jun 2020 23:15:56: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 23:16:01: 26000000 INFO @ Sun, 21 Jun 2020 23:16:02: 19000000 INFO @ Sun, 21 Jun 2020 23:16:06: 27000000 INFO @ Sun, 21 Jun 2020 23:16:08: 20000000 INFO @ Sun, 21 Jun 2020 23:16:11: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 23:16:11: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 23:16:11: #1 total tags in treatment: 27818459 INFO @ Sun, 21 Jun 2020 23:16:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 23:16:11: #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 23:16:12: #1 tags after filtering in treatment: 27818458 INFO @ Sun, 21 Jun 2020 23:16:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 23:16:12: #1 finished! INFO @ Sun, 21 Jun 2020 23:16:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 23:16:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 23:16:14: #2 number of paired peaks: 240 WARNING @ Sun, 21 Jun 2020 23:16:14: Fewer paired peaks (240) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 240 pairs to build model! INFO @ Sun, 21 Jun 2020 23:16:14: start model_add_line... INFO @ Sun, 21 Jun 2020 23:16:14: start X-correlation... INFO @ Sun, 21 Jun 2020 23:16:14: end of X-cor INFO @ Sun, 21 Jun 2020 23:16:14: #2 finished! INFO @ Sun, 21 Jun 2020 23:16:14: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 23:16:14: #2 alternative fragment length(s) may be 1,12,19,38,557 bps INFO @ Sun, 21 Jun 2020 23:16:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX969929/SRX969929.10_model.r WARNING @ Sun, 21 Jun 2020 23:16:14: #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 23:16:14: #2 You may need to consider one of the other alternative d(s): 1,12,19,38,557 WARNING @ Sun, 21 Jun 2020 23:16:14: #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 23:16:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 23:16:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 23:16:14: 21000000 INFO @ Sun, 21 Jun 2020 23:16:20: 22000000 INFO @ Sun, 21 Jun 2020 23:16:26: 23000000 INFO @ Sun, 21 Jun 2020 23:16:32: 24000000 INFO @ Sun, 21 Jun 2020 23:16:38: 25000000 INFO @ Sun, 21 Jun 2020 23:16:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 23:16:44: 26000000 INFO @ Sun, 21 Jun 2020 23:16:50: 27000000 INFO @ Sun, 21 Jun 2020 23:16:55: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 23:16:55: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 23:16:55: #1 total tags in treatment: 27818459 INFO @ Sun, 21 Jun 2020 23:16:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 23:16:55: #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 23:16:56: #1 tags after filtering in treatment: 27818458 INFO @ Sun, 21 Jun 2020 23:16:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 23:16:56: #1 finished! INFO @ Sun, 21 Jun 2020 23:16:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 23:16:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 23:16:57: #2 number of paired peaks: 240 WARNING @ Sun, 21 Jun 2020 23:16:57: Fewer paired peaks (240) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 240 pairs to build model! INFO @ Sun, 21 Jun 2020 23:16:57: start model_add_line... INFO @ Sun, 21 Jun 2020 23:16:57: start X-correlation... INFO @ Sun, 21 Jun 2020 23:16:57: end of X-cor INFO @ Sun, 21 Jun 2020 23:16:57: #2 finished! INFO @ Sun, 21 Jun 2020 23:16:57: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 23:16:57: #2 alternative fragment length(s) may be 1,12,19,38,557 bps INFO @ Sun, 21 Jun 2020 23:16:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX969929/SRX969929.20_model.r WARNING @ Sun, 21 Jun 2020 23:16:57: #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 23:16:57: #2 You may need to consider one of the other alternative d(s): 1,12,19,38,557 WARNING @ Sun, 21 Jun 2020 23:16:57: #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 23:16:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 23:16:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 23:16:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX969929/SRX969929.05_peaks.xls INFO @ Sun, 21 Jun 2020 23:16:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX969929/SRX969929.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 23:16:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX969929/SRX969929.05_summits.bed INFO @ Sun, 21 Jun 2020 23:16:59: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 23:16:59: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 23:17:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX969929/SRX969929.10_peaks.xls INFO @ Sun, 21 Jun 2020 23:17:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX969929/SRX969929.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 23:17:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX969929/SRX969929.10_summits.bed INFO @ Sun, 21 Jun 2020 23:17:19: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 23:17:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 23:18:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX969929/SRX969929.20_peaks.xls INFO @ Sun, 21 Jun 2020 23:18:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX969929/SRX969929.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 23:18:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX969929/SRX969929.20_summits.bed INFO @ Sun, 21 Jun 2020 23:18:01: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling