Job ID = 6456627 SRX = SRX375352 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:04:01 prefetch.2.10.7: 1) Downloading 'SRR1027842'... 2020-06-21T11:04:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:10:30 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:10:30 prefetch.2.10.7: 1) 'SRR1027842' was downloaded successfully Read 38060396 spots for SRR1027842/SRR1027842.sra Written 38060396 spots for SRR1027842/SRR1027842.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: 00:10:39 38060396 reads; of these: 38060396 (100.00%) were unpaired; of these: 3224643 (8.47%) aligned 0 times 26152302 (68.71%) aligned exactly 1 time 8683451 (22.81%) aligned >1 times 91.53% overall alignment rate Time searching: 00:10:39 Overall time: 00:10:39 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] 8333095 / 34835753 = 0.2392 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 20:31:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX375352/SRX375352.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX375352/SRX375352.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX375352/SRX375352.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX375352/SRX375352.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 20:31:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:31:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:31:10: 1000000 INFO @ Sun, 21 Jun 2020 20:31:16: 2000000 INFO @ Sun, 21 Jun 2020 20:31:22: 3000000 INFO @ Sun, 21 Jun 2020 20:31:28: 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 20:31:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX375352/SRX375352.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX375352/SRX375352.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX375352/SRX375352.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX375352/SRX375352.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 20:31:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:31:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:31:34: 5000000 INFO @ Sun, 21 Jun 2020 20:31:40: 6000000 INFO @ Sun, 21 Jun 2020 20:31:40: 1000000 INFO @ Sun, 21 Jun 2020 20:31:47: 2000000 INFO @ Sun, 21 Jun 2020 20:31:47: 7000000 INFO @ Sun, 21 Jun 2020 20:31:53: 3000000 INFO @ Sun, 21 Jun 2020 20:31:54: 8000000 INFO @ Sun, 21 Jun 2020 20:32:00: 4000000 INFO @ Sun, 21 Jun 2020 20:32:00: 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 20:32:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX375352/SRX375352.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX375352/SRX375352.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX375352/SRX375352.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX375352/SRX375352.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 20:32:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:32:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:32:07: 10000000 INFO @ Sun, 21 Jun 2020 20:32:07: 5000000 INFO @ Sun, 21 Jun 2020 20:32:10: 1000000 INFO @ Sun, 21 Jun 2020 20:32:13: 11000000 INFO @ Sun, 21 Jun 2020 20:32:14: 6000000 INFO @ Sun, 21 Jun 2020 20:32:17: 2000000 INFO @ Sun, 21 Jun 2020 20:32:20: 12000000 INFO @ Sun, 21 Jun 2020 20:32:20: 7000000 INFO @ Sun, 21 Jun 2020 20:32:24: 3000000 INFO @ Sun, 21 Jun 2020 20:32:27: 13000000 INFO @ Sun, 21 Jun 2020 20:32:27: 8000000 INFO @ Sun, 21 Jun 2020 20:32:30: 4000000 INFO @ Sun, 21 Jun 2020 20:32:33: 14000000 INFO @ Sun, 21 Jun 2020 20:32:33: 9000000 INFO @ Sun, 21 Jun 2020 20:32:37: 5000000 INFO @ Sun, 21 Jun 2020 20:32:40: 10000000 INFO @ Sun, 21 Jun 2020 20:32:41: 15000000 INFO @ Sun, 21 Jun 2020 20:32:44: 6000000 INFO @ Sun, 21 Jun 2020 20:32:47: 11000000 INFO @ Sun, 21 Jun 2020 20:32:48: 16000000 INFO @ Sun, 21 Jun 2020 20:32:50: 7000000 INFO @ Sun, 21 Jun 2020 20:32:53: 12000000 INFO @ Sun, 21 Jun 2020 20:32:55: 17000000 INFO @ Sun, 21 Jun 2020 20:32:57: 8000000 INFO @ Sun, 21 Jun 2020 20:33:00: 13000000 INFO @ Sun, 21 Jun 2020 20:33:02: 18000000 INFO @ Sun, 21 Jun 2020 20:33:03: 9000000 INFO @ Sun, 21 Jun 2020 20:33:07: 14000000 INFO @ Sun, 21 Jun 2020 20:33:09: 19000000 INFO @ Sun, 21 Jun 2020 20:33:10: 10000000 INFO @ Sun, 21 Jun 2020 20:33:14: 15000000 INFO @ Sun, 21 Jun 2020 20:33:15: 20000000 INFO @ Sun, 21 Jun 2020 20:33:17: 11000000 INFO @ Sun, 21 Jun 2020 20:33:21: 16000000 INFO @ Sun, 21 Jun 2020 20:33:23: 21000000 INFO @ Sun, 21 Jun 2020 20:33:23: 12000000 INFO @ Sun, 21 Jun 2020 20:33:28: 17000000 INFO @ Sun, 21 Jun 2020 20:33:30: 22000000 INFO @ Sun, 21 Jun 2020 20:33:30: 13000000 INFO @ Sun, 21 Jun 2020 20:33:34: 18000000 INFO @ Sun, 21 Jun 2020 20:33:37: 14000000 INFO @ Sun, 21 Jun 2020 20:33:37: 23000000 INFO @ Sun, 21 Jun 2020 20:33:41: 19000000 INFO @ Sun, 21 Jun 2020 20:33:44: 15000000 INFO @ Sun, 21 Jun 2020 20:33:44: 24000000 INFO @ Sun, 21 Jun 2020 20:33:48: 20000000 INFO @ Sun, 21 Jun 2020 20:33:50: 16000000 INFO @ Sun, 21 Jun 2020 20:33:51: 25000000 INFO @ Sun, 21 Jun 2020 20:33:55: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:33:57: 17000000 INFO @ Sun, 21 Jun 2020 20:33:58: 26000000 INFO @ Sun, 21 Jun 2020 20:34:02: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:34:02: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:34:02: #1 total tags in treatment: 26502658 INFO @ Sun, 21 Jun 2020 20:34:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:34:02: #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 20:34:02: 22000000 INFO @ Sun, 21 Jun 2020 20:34:03: #1 tags after filtering in treatment: 26502656 INFO @ Sun, 21 Jun 2020 20:34:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:34:03: #1 finished! INFO @ Sun, 21 Jun 2020 20:34:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:34:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:34:04: 18000000 INFO @ Sun, 21 Jun 2020 20:34:04: #2 number of paired peaks: 390 WARNING @ Sun, 21 Jun 2020 20:34:04: Fewer paired peaks (390) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 390 pairs to build model! INFO @ Sun, 21 Jun 2020 20:34:04: start model_add_line... INFO @ Sun, 21 Jun 2020 20:34:04: start X-correlation... INFO @ Sun, 21 Jun 2020 20:34:04: end of X-cor INFO @ Sun, 21 Jun 2020 20:34:04: #2 finished! INFO @ Sun, 21 Jun 2020 20:34:04: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 20:34:04: #2 alternative fragment length(s) may be 2 bps INFO @ Sun, 21 Jun 2020 20:34:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX375352/SRX375352.05_model.r WARNING @ Sun, 21 Jun 2020 20:34:04: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:34:04: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Sun, 21 Jun 2020 20:34:04: #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 20:34:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:34:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:34:09: 23000000 INFO @ Sun, 21 Jun 2020 20:34:10: 19000000 INFO @ Sun, 21 Jun 2020 20:34:15: 24000000 INFO @ Sun, 21 Jun 2020 20:34:17: 20000000 INFO @ Sun, 21 Jun 2020 20:34:22: 25000000 INFO @ Sun, 21 Jun 2020 20:34:24: 21000000 INFO @ Sun, 21 Jun 2020 20:34:29: 26000000 INFO @ Sun, 21 Jun 2020 20:34:31: 22000000 INFO @ Sun, 21 Jun 2020 20:34:32: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:34:32: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:34:32: #1 total tags in treatment: 26502658 INFO @ Sun, 21 Jun 2020 20:34:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:34:32: #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 20:34:33: #1 tags after filtering in treatment: 26502656 INFO @ Sun, 21 Jun 2020 20:34:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:34:33: #1 finished! INFO @ Sun, 21 Jun 2020 20:34:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:34:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:34:35: #2 number of paired peaks: 390 WARNING @ Sun, 21 Jun 2020 20:34:35: Fewer paired peaks (390) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 390 pairs to build model! INFO @ Sun, 21 Jun 2020 20:34:35: start model_add_line... INFO @ Sun, 21 Jun 2020 20:34:35: start X-correlation... INFO @ Sun, 21 Jun 2020 20:34:35: end of X-cor INFO @ Sun, 21 Jun 2020 20:34:35: #2 finished! INFO @ Sun, 21 Jun 2020 20:34:35: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 20:34:35: #2 alternative fragment length(s) may be 2 bps INFO @ Sun, 21 Jun 2020 20:34:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX375352/SRX375352.10_model.r WARNING @ Sun, 21 Jun 2020 20:34:35: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:34:35: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Sun, 21 Jun 2020 20:34:35: #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 20:34:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:34:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:34:37: 23000000 INFO @ Sun, 21 Jun 2020 20:34:43: 24000000 INFO @ Sun, 21 Jun 2020 20:34:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:34:50: 25000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:34:56: 26000000 INFO @ Sun, 21 Jun 2020 20:34:59: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:34:59: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:34:59: #1 total tags in treatment: 26502658 INFO @ Sun, 21 Jun 2020 20:34:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:34:59: #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 20:35:00: #1 tags after filtering in treatment: 26502656 INFO @ Sun, 21 Jun 2020 20:35:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:35:00: #1 finished! INFO @ Sun, 21 Jun 2020 20:35:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:35:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:35:02: #2 number of paired peaks: 390 WARNING @ Sun, 21 Jun 2020 20:35:02: Fewer paired peaks (390) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 390 pairs to build model! INFO @ Sun, 21 Jun 2020 20:35:02: start model_add_line... INFO @ Sun, 21 Jun 2020 20:35:02: start X-correlation... INFO @ Sun, 21 Jun 2020 20:35:02: end of X-cor INFO @ Sun, 21 Jun 2020 20:35:02: #2 finished! INFO @ Sun, 21 Jun 2020 20:35:02: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 20:35:02: #2 alternative fragment length(s) may be 2 bps INFO @ Sun, 21 Jun 2020 20:35:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX375352/SRX375352.20_model.r WARNING @ Sun, 21 Jun 2020 20:35:02: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:35:02: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Sun, 21 Jun 2020 20:35:02: #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 20:35:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:35:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:35:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX375352/SRX375352.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:35:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX375352/SRX375352.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:35:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX375352/SRX375352.05_summits.bed INFO @ Sun, 21 Jun 2020 20:35:05: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:35:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:35:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX375352/SRX375352.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:35:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX375352/SRX375352.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:35:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX375352/SRX375352.10_summits.bed INFO @ Sun, 21 Jun 2020 20:35:37: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:35:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:36:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX375352/SRX375352.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:36:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX375352/SRX375352.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:36:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX375352/SRX375352.20_summits.bed INFO @ Sun, 21 Jun 2020 20:36:04: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling