Job ID = 6454763 SRX = SRX2564145 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:30:14 prefetch.2.10.7: 1) Downloading 'SRR5259264'... 2020-06-21T09:30:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:37:02 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:37:02 prefetch.2.10.7: 1) 'SRR5259264' was downloaded successfully 2020-06-21T09:37:02 prefetch.2.10.7: 'SRR5259264' has 0 unresolved dependencies Read 43923803 spots for SRR5259264/SRR5259264.sra Written 43923803 spots for SRR5259264/SRR5259264.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: 00:15:52 43923803 reads; of these: 43923803 (100.00%) were unpaired; of these: 7601563 (17.31%) aligned 0 times 26745836 (60.89%) aligned exactly 1 time 9576404 (21.80%) aligned >1 times 82.69% overall alignment rate Time searching: 00:15:52 Overall time: 00:15:52 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] 9306555 / 36322240 = 0.2562 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 19:08:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2564145/SRX2564145.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2564145/SRX2564145.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2564145/SRX2564145.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2564145/SRX2564145.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 19:08:01: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:08:01: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:08:08: 1000000 INFO @ Sun, 21 Jun 2020 19:08:17: 2000000 INFO @ Sun, 21 Jun 2020 19:08:27: 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 19:08:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2564145/SRX2564145.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2564145/SRX2564145.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2564145/SRX2564145.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2564145/SRX2564145.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 19:08:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:08:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:08:36: 4000000 INFO @ Sun, 21 Jun 2020 19:08:39: 1000000 INFO @ Sun, 21 Jun 2020 19:08:44: 5000000 INFO @ Sun, 21 Jun 2020 19:08:48: 2000000 INFO @ Sun, 21 Jun 2020 19:08:53: 6000000 INFO @ Sun, 21 Jun 2020 19:08:56: 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 19:09:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2564145/SRX2564145.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2564145/SRX2564145.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2564145/SRX2564145.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2564145/SRX2564145.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 19:09:01: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:09:01: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:09:02: 7000000 INFO @ Sun, 21 Jun 2020 19:09:04: 4000000 INFO @ Sun, 21 Jun 2020 19:09:10: 1000000 INFO @ Sun, 21 Jun 2020 19:09:11: 8000000 INFO @ Sun, 21 Jun 2020 19:09:13: 5000000 INFO @ Sun, 21 Jun 2020 19:09:18: 2000000 INFO @ Sun, 21 Jun 2020 19:09:20: 9000000 INFO @ Sun, 21 Jun 2020 19:09:22: 6000000 INFO @ Sun, 21 Jun 2020 19:09:27: 3000000 INFO @ Sun, 21 Jun 2020 19:09:29: 10000000 INFO @ Sun, 21 Jun 2020 19:09:30: 7000000 INFO @ Sun, 21 Jun 2020 19:09:36: 4000000 INFO @ Sun, 21 Jun 2020 19:09:38: 11000000 INFO @ Sun, 21 Jun 2020 19:09:39: 8000000 INFO @ Sun, 21 Jun 2020 19:09:44: 5000000 INFO @ Sun, 21 Jun 2020 19:09:47: 9000000 INFO @ Sun, 21 Jun 2020 19:09:49: 12000000 INFO @ Sun, 21 Jun 2020 19:09:53: 6000000 INFO @ Sun, 21 Jun 2020 19:09:55: 10000000 INFO @ Sun, 21 Jun 2020 19:09:57: 13000000 INFO @ Sun, 21 Jun 2020 19:10:01: 7000000 INFO @ Sun, 21 Jun 2020 19:10:03: 11000000 INFO @ Sun, 21 Jun 2020 19:10:07: 14000000 INFO @ Sun, 21 Jun 2020 19:10:09: 8000000 INFO @ Sun, 21 Jun 2020 19:10:11: 12000000 INFO @ Sun, 21 Jun 2020 19:10:16: 15000000 INFO @ Sun, 21 Jun 2020 19:10:17: 9000000 INFO @ Sun, 21 Jun 2020 19:10:19: 13000000 INFO @ Sun, 21 Jun 2020 19:10:24: 10000000 INFO @ Sun, 21 Jun 2020 19:10:26: 16000000 INFO @ Sun, 21 Jun 2020 19:10:28: 14000000 INFO @ Sun, 21 Jun 2020 19:10:32: 11000000 INFO @ Sun, 21 Jun 2020 19:10:35: 17000000 INFO @ Sun, 21 Jun 2020 19:10:36: 15000000 INFO @ Sun, 21 Jun 2020 19:10:38: 12000000 INFO @ Sun, 21 Jun 2020 19:10:43: 18000000 INFO @ Sun, 21 Jun 2020 19:10:44: 16000000 INFO @ Sun, 21 Jun 2020 19:10:45: 13000000 INFO @ Sun, 21 Jun 2020 19:10:51: 14000000 INFO @ Sun, 21 Jun 2020 19:10:51: 19000000 INFO @ Sun, 21 Jun 2020 19:10:52: 17000000 INFO @ Sun, 21 Jun 2020 19:10:57: 15000000 INFO @ Sun, 21 Jun 2020 19:10:59: 20000000 INFO @ Sun, 21 Jun 2020 19:11:01: 18000000 INFO @ Sun, 21 Jun 2020 19:11:04: 16000000 INFO @ Sun, 21 Jun 2020 19:11:07: 21000000 INFO @ Sun, 21 Jun 2020 19:11:08: 19000000 INFO @ Sun, 21 Jun 2020 19:11:11: 17000000 INFO @ Sun, 21 Jun 2020 19:11:14: 20000000 INFO @ Sun, 21 Jun 2020 19:11:17: 22000000 INFO @ Sun, 21 Jun 2020 19:11:18: 18000000 INFO @ Sun, 21 Jun 2020 19:11:21: 21000000 INFO @ Sun, 21 Jun 2020 19:11:25: 23000000 INFO @ Sun, 21 Jun 2020 19:11:25: 19000000 INFO @ Sun, 21 Jun 2020 19:11:28: 22000000 INFO @ Sun, 21 Jun 2020 19:11:33: 24000000 INFO @ Sun, 21 Jun 2020 19:11:33: 20000000 INFO @ Sun, 21 Jun 2020 19:11:35: 23000000 INFO @ Sun, 21 Jun 2020 19:11:41: 25000000 INFO @ Sun, 21 Jun 2020 19:11:41: 21000000 INFO @ Sun, 21 Jun 2020 19:11:42: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:11:48: 25000000 INFO @ Sun, 21 Jun 2020 19:11:49: 26000000 INFO @ Sun, 21 Jun 2020 19:11:50: 22000000 INFO @ Sun, 21 Jun 2020 19:11:55: 26000000 INFO @ Sun, 21 Jun 2020 19:11:57: 27000000 INFO @ Sun, 21 Jun 2020 19:11:58: #1 tag size is determined as 74 bps INFO @ Sun, 21 Jun 2020 19:11:58: #1 tag size = 74 INFO @ Sun, 21 Jun 2020 19:11:58: #1 total tags in treatment: 27015685 INFO @ Sun, 21 Jun 2020 19:11:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:11:58: #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 19:11:58: 23000000 INFO @ Sun, 21 Jun 2020 19:11:59: #1 tags after filtering in treatment: 27015685 INFO @ Sun, 21 Jun 2020 19:11:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:11:59: #1 finished! INFO @ Sun, 21 Jun 2020 19:11:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:11:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:12:01: #2 number of paired peaks: 486 WARNING @ Sun, 21 Jun 2020 19:12:01: Fewer paired peaks (486) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 486 pairs to build model! INFO @ Sun, 21 Jun 2020 19:12:01: start model_add_line... INFO @ Sun, 21 Jun 2020 19:12:01: start X-correlation... INFO @ Sun, 21 Jun 2020 19:12:01: end of X-cor INFO @ Sun, 21 Jun 2020 19:12:01: #2 finished! INFO @ Sun, 21 Jun 2020 19:12:01: #2 predicted fragment length is 3 bps INFO @ Sun, 21 Jun 2020 19:12:01: #2 alternative fragment length(s) may be 3,23,34 bps INFO @ Sun, 21 Jun 2020 19:12:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2564145/SRX2564145.05_model.r WARNING @ Sun, 21 Jun 2020 19:12:01: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:12:01: #2 You may need to consider one of the other alternative d(s): 3,23,34 WARNING @ Sun, 21 Jun 2020 19:12:01: #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 19:12:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:12:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:12:01: 27000000 INFO @ Sun, 21 Jun 2020 19:12:02: #1 tag size is determined as 74 bps INFO @ Sun, 21 Jun 2020 19:12:02: #1 tag size = 74 INFO @ Sun, 21 Jun 2020 19:12:02: #1 total tags in treatment: 27015685 INFO @ Sun, 21 Jun 2020 19:12:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:12:02: #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 19:12:03: #1 tags after filtering in treatment: 27015685 INFO @ Sun, 21 Jun 2020 19:12:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:12:03: #1 finished! INFO @ Sun, 21 Jun 2020 19:12:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:12:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:12:05: #2 number of paired peaks: 486 WARNING @ Sun, 21 Jun 2020 19:12:05: Fewer paired peaks (486) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 486 pairs to build model! INFO @ Sun, 21 Jun 2020 19:12:05: start model_add_line... INFO @ Sun, 21 Jun 2020 19:12:05: start X-correlation... INFO @ Sun, 21 Jun 2020 19:12:05: end of X-cor INFO @ Sun, 21 Jun 2020 19:12:05: #2 finished! INFO @ Sun, 21 Jun 2020 19:12:05: #2 predicted fragment length is 3 bps INFO @ Sun, 21 Jun 2020 19:12:05: #2 alternative fragment length(s) may be 3,23,34 bps INFO @ Sun, 21 Jun 2020 19:12:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2564145/SRX2564145.10_model.r WARNING @ Sun, 21 Jun 2020 19:12:05: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:12:05: #2 You may need to consider one of the other alternative d(s): 3,23,34 WARNING @ Sun, 21 Jun 2020 19:12:05: #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 19:12:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:12:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:12:07: 24000000 INFO @ Sun, 21 Jun 2020 19:12:15: 25000000 INFO @ Sun, 21 Jun 2020 19:12:23: 26000000 INFO @ Sun, 21 Jun 2020 19:12:33: 27000000 INFO @ Sun, 21 Jun 2020 19:12:33: #1 tag size is determined as 74 bps INFO @ Sun, 21 Jun 2020 19:12:33: #1 tag size = 74 INFO @ Sun, 21 Jun 2020 19:12:33: #1 total tags in treatment: 27015685 INFO @ Sun, 21 Jun 2020 19:12:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:12:33: #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 19:12:34: #1 tags after filtering in treatment: 27015685 INFO @ Sun, 21 Jun 2020 19:12:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:12:34: #1 finished! INFO @ Sun, 21 Jun 2020 19:12:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:12:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:12:36: #2 number of paired peaks: 486 WARNING @ Sun, 21 Jun 2020 19:12:36: Fewer paired peaks (486) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 486 pairs to build model! INFO @ Sun, 21 Jun 2020 19:12:36: start model_add_line... INFO @ Sun, 21 Jun 2020 19:12:36: start X-correlation... INFO @ Sun, 21 Jun 2020 19:12:36: end of X-cor INFO @ Sun, 21 Jun 2020 19:12:36: #2 finished! INFO @ Sun, 21 Jun 2020 19:12:36: #2 predicted fragment length is 3 bps INFO @ Sun, 21 Jun 2020 19:12:36: #2 alternative fragment length(s) may be 3,23,34 bps INFO @ Sun, 21 Jun 2020 19:12:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2564145/SRX2564145.20_model.r WARNING @ Sun, 21 Jun 2020 19:12:36: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:12:36: #2 You may need to consider one of the other alternative d(s): 3,23,34 WARNING @ Sun, 21 Jun 2020 19:12:36: #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 19:12:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:12:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:12:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:12:43: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:13:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2564145/SRX2564145.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:13:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2564145/SRX2564145.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:13:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2564145/SRX2564145.05_summits.bed INFO @ Sun, 21 Jun 2020 19:13:02: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:13:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2564145/SRX2564145.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:13:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2564145/SRX2564145.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:13:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2564145/SRX2564145.10_summits.bed INFO @ Sun, 21 Jun 2020 19:13:02: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:13:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:13:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2564145/SRX2564145.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:13:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2564145/SRX2564145.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:13:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2564145/SRX2564145.20_summits.bed INFO @ Sun, 21 Jun 2020 19:13:36: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling