Job ID = 6456044 SRX = SRX3159494 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:33:19 prefetch.2.10.7: 1) Downloading 'SRR6004224'... 2020-06-21T10:33:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:38:02 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:38:02 prefetch.2.10.7: 1) 'SRR6004224' was downloaded successfully 2020-06-21T10:38:02 prefetch.2.10.7: 'SRR6004224' has 0 unresolved dependencies Read 49067644 spots for SRR6004224/SRR6004224.sra Written 49067644 spots for SRR6004224/SRR6004224.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: 00:14:42 49067644 reads; of these: 49067644 (100.00%) were unpaired; of these: 1801813 (3.67%) aligned 0 times 32265931 (65.76%) aligned exactly 1 time 14999900 (30.57%) aligned >1 times 96.33% overall alignment rate Time searching: 00:14:42 Overall time: 00:14:42 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 20 files... [bam_rmdupse_core] 10058267 / 47265831 = 0.2128 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 20:03:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3159494/SRX3159494.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3159494/SRX3159494.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3159494/SRX3159494.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3159494/SRX3159494.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 20:03:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:03:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:03:57: 1000000 INFO @ Sun, 21 Jun 2020 20:04:03: 2000000 INFO @ Sun, 21 Jun 2020 20:04:08: 3000000 INFO @ Sun, 21 Jun 2020 20:04:13: 4000000 INFO @ Sun, 21 Jun 2020 20:04:19: 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 @ Sun, 21 Jun 2020 20:04:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3159494/SRX3159494.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3159494/SRX3159494.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3159494/SRX3159494.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3159494/SRX3159494.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 20:04:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:04:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:04:24: 6000000 INFO @ Sun, 21 Jun 2020 20:04:28: 1000000 INFO @ Sun, 21 Jun 2020 20:04:30: 7000000 INFO @ Sun, 21 Jun 2020 20:04:34: 2000000 INFO @ Sun, 21 Jun 2020 20:04:36: 8000000 INFO @ Sun, 21 Jun 2020 20:04:40: 3000000 INFO @ Sun, 21 Jun 2020 20:04:42: 9000000 INFO @ Sun, 21 Jun 2020 20:04:46: 4000000 INFO @ Sun, 21 Jun 2020 20:04:48: 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 @ Sun, 21 Jun 2020 20:04:52: 5000000 INFO @ Sun, 21 Jun 2020 20:04:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3159494/SRX3159494.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3159494/SRX3159494.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3159494/SRX3159494.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3159494/SRX3159494.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 20:04:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:04:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:04:54: 11000000 INFO @ Sun, 21 Jun 2020 20:04:58: 6000000 INFO @ Sun, 21 Jun 2020 20:04:58: 1000000 INFO @ Sun, 21 Jun 2020 20:05:00: 12000000 INFO @ Sun, 21 Jun 2020 20:05:04: 7000000 INFO @ Sun, 21 Jun 2020 20:05:04: 2000000 INFO @ Sun, 21 Jun 2020 20:05:06: 13000000 INFO @ Sun, 21 Jun 2020 20:05:10: 8000000 INFO @ Sun, 21 Jun 2020 20:05:10: 3000000 INFO @ Sun, 21 Jun 2020 20:05:12: 14000000 INFO @ Sun, 21 Jun 2020 20:05:16: 9000000 INFO @ Sun, 21 Jun 2020 20:05:16: 4000000 INFO @ Sun, 21 Jun 2020 20:05:18: 15000000 INFO @ Sun, 21 Jun 2020 20:05:22: 10000000 INFO @ Sun, 21 Jun 2020 20:05:22: 5000000 INFO @ Sun, 21 Jun 2020 20:05:24: 16000000 INFO @ Sun, 21 Jun 2020 20:05:28: 11000000 INFO @ Sun, 21 Jun 2020 20:05:28: 6000000 INFO @ Sun, 21 Jun 2020 20:05:30: 17000000 INFO @ Sun, 21 Jun 2020 20:05:34: 12000000 INFO @ Sun, 21 Jun 2020 20:05:34: 7000000 INFO @ Sun, 21 Jun 2020 20:05:37: 18000000 INFO @ Sun, 21 Jun 2020 20:05:40: 13000000 INFO @ Sun, 21 Jun 2020 20:05:40: 8000000 INFO @ Sun, 21 Jun 2020 20:05:43: 19000000 INFO @ Sun, 21 Jun 2020 20:05:46: 14000000 INFO @ Sun, 21 Jun 2020 20:05:46: 9000000 INFO @ Sun, 21 Jun 2020 20:05:49: 20000000 INFO @ Sun, 21 Jun 2020 20:05:52: 15000000 INFO @ Sun, 21 Jun 2020 20:05:52: 10000000 INFO @ Sun, 21 Jun 2020 20:05:55: 21000000 INFO @ Sun, 21 Jun 2020 20:05:58: 16000000 INFO @ Sun, 21 Jun 2020 20:05:58: 11000000 INFO @ Sun, 21 Jun 2020 20:06:01: 22000000 INFO @ Sun, 21 Jun 2020 20:06:04: 17000000 INFO @ Sun, 21 Jun 2020 20:06:04: 12000000 INFO @ Sun, 21 Jun 2020 20:06:07: 23000000 INFO @ Sun, 21 Jun 2020 20:06:10: 18000000 INFO @ Sun, 21 Jun 2020 20:06:10: 13000000 INFO @ Sun, 21 Jun 2020 20:06:13: 24000000 INFO @ Sun, 21 Jun 2020 20:06:16: 19000000 INFO @ Sun, 21 Jun 2020 20:06:16: 14000000 INFO @ Sun, 21 Jun 2020 20:06:19: 25000000 INFO @ Sun, 21 Jun 2020 20:06:22: 20000000 INFO @ Sun, 21 Jun 2020 20:06:22: 15000000 INFO @ Sun, 21 Jun 2020 20:06:25: 26000000 INFO @ Sun, 21 Jun 2020 20:06:28: 21000000 INFO @ Sun, 21 Jun 2020 20:06:28: 16000000 INFO @ Sun, 21 Jun 2020 20:06:31: 27000000 INFO @ Sun, 21 Jun 2020 20:06:34: 22000000 INFO @ Sun, 21 Jun 2020 20:06:34: 17000000 INFO @ Sun, 21 Jun 2020 20:06:37: 28000000 INFO @ Sun, 21 Jun 2020 20:06:40: 23000000 INFO @ Sun, 21 Jun 2020 20:06:40: 18000000 INFO @ Sun, 21 Jun 2020 20:06:43: 29000000 INFO @ Sun, 21 Jun 2020 20:06:46: 24000000 INFO @ Sun, 21 Jun 2020 20:06:46: 19000000 INFO @ Sun, 21 Jun 2020 20:06:49: 30000000 INFO @ Sun, 21 Jun 2020 20:06:52: 25000000 INFO @ Sun, 21 Jun 2020 20:06:52: 20000000 INFO @ Sun, 21 Jun 2020 20:06:55: 31000000 INFO @ Sun, 21 Jun 2020 20:06:58: 26000000 INFO @ Sun, 21 Jun 2020 20:06:58: 21000000 INFO @ Sun, 21 Jun 2020 20:07:01: 32000000 INFO @ Sun, 21 Jun 2020 20:07:04: 27000000 INFO @ Sun, 21 Jun 2020 20:07:04: 22000000 INFO @ Sun, 21 Jun 2020 20:07:07: 33000000 INFO @ Sun, 21 Jun 2020 20:07:10: 28000000 INFO @ Sun, 21 Jun 2020 20:07:10: 23000000 INFO @ Sun, 21 Jun 2020 20:07:13: 34000000 INFO @ Sun, 21 Jun 2020 20:07:16: 29000000 INFO @ Sun, 21 Jun 2020 20:07:16: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:07:19: 35000000 INFO @ Sun, 21 Jun 2020 20:07:22: 30000000 INFO @ Sun, 21 Jun 2020 20:07:22: 25000000 INFO @ Sun, 21 Jun 2020 20:07:25: 36000000 INFO @ Sun, 21 Jun 2020 20:07:28: 31000000 INFO @ Sun, 21 Jun 2020 20:07:28: 26000000 INFO @ Sun, 21 Jun 2020 20:07:32: 37000000 INFO @ Sun, 21 Jun 2020 20:07:33: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:07:33: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:07:33: #1 total tags in treatment: 37207564 INFO @ Sun, 21 Jun 2020 20:07:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:07:33: #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 20:07:34: 32000000 INFO @ Sun, 21 Jun 2020 20:07:34: #1 tags after filtering in treatment: 37207563 INFO @ Sun, 21 Jun 2020 20:07:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:07:34: #1 finished! INFO @ Sun, 21 Jun 2020 20:07:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:07:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:07:34: 27000000 INFO @ Sun, 21 Jun 2020 20:07:36: #2 number of paired peaks: 120 WARNING @ Sun, 21 Jun 2020 20:07:36: Fewer paired peaks (120) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 120 pairs to build model! INFO @ Sun, 21 Jun 2020 20:07:36: start model_add_line... INFO @ Sun, 21 Jun 2020 20:07:36: start X-correlation... INFO @ Sun, 21 Jun 2020 20:07:36: end of X-cor INFO @ Sun, 21 Jun 2020 20:07:36: #2 finished! INFO @ Sun, 21 Jun 2020 20:07:36: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 20:07:36: #2 alternative fragment length(s) may be 2,45 bps INFO @ Sun, 21 Jun 2020 20:07:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3159494/SRX3159494.05_model.r WARNING @ Sun, 21 Jun 2020 20:07:36: #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 20:07:36: #2 You may need to consider one of the other alternative d(s): 2,45 WARNING @ Sun, 21 Jun 2020 20:07:36: #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 20:07:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:07:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:07:40: 33000000 INFO @ Sun, 21 Jun 2020 20:07:40: 28000000 INFO @ Sun, 21 Jun 2020 20:07:46: 34000000 INFO @ Sun, 21 Jun 2020 20:07:46: 29000000 INFO @ Sun, 21 Jun 2020 20:07:52: 35000000 INFO @ Sun, 21 Jun 2020 20:07:52: 30000000 INFO @ Sun, 21 Jun 2020 20:07:58: 36000000 INFO @ Sun, 21 Jun 2020 20:07:58: 31000000 INFO @ Sun, 21 Jun 2020 20:08:04: 37000000 INFO @ Sun, 21 Jun 2020 20:08:04: 32000000 INFO @ Sun, 21 Jun 2020 20:08:05: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:08:05: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:08:05: #1 total tags in treatment: 37207564 INFO @ Sun, 21 Jun 2020 20:08:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:08:05: #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 20:08:06: #1 tags after filtering in treatment: 37207563 INFO @ Sun, 21 Jun 2020 20:08:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:08:06: #1 finished! INFO @ Sun, 21 Jun 2020 20:08:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:08:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:08:08: #2 number of paired peaks: 120 WARNING @ Sun, 21 Jun 2020 20:08:08: Fewer paired peaks (120) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 120 pairs to build model! INFO @ Sun, 21 Jun 2020 20:08:08: start model_add_line... INFO @ Sun, 21 Jun 2020 20:08:08: start X-correlation... INFO @ Sun, 21 Jun 2020 20:08:08: end of X-cor INFO @ Sun, 21 Jun 2020 20:08:08: #2 finished! INFO @ Sun, 21 Jun 2020 20:08:08: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 20:08:08: #2 alternative fragment length(s) may be 2,45 bps INFO @ Sun, 21 Jun 2020 20:08:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3159494/SRX3159494.10_model.r WARNING @ Sun, 21 Jun 2020 20:08:08: #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 20:08:08: #2 You may need to consider one of the other alternative d(s): 2,45 WARNING @ Sun, 21 Jun 2020 20:08:08: #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 20:08:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:08:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:08:10: 33000000 INFO @ Sun, 21 Jun 2020 20:08:16: 34000000 INFO @ Sun, 21 Jun 2020 20:08:21: 35000000 INFO @ Sun, 21 Jun 2020 20:08:27: 36000000 INFO @ Sun, 21 Jun 2020 20:08:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:08:32: 37000000 INFO @ Sun, 21 Jun 2020 20:08:33: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:08:33: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:08:33: #1 total tags in treatment: 37207564 INFO @ Sun, 21 Jun 2020 20:08:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:08:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:08:34: #1 tags after filtering in treatment: 37207563 INFO @ Sun, 21 Jun 2020 20:08:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:08:34: #1 finished! INFO @ Sun, 21 Jun 2020 20:08:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:08:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:08:36: #2 number of paired peaks: 120 WARNING @ Sun, 21 Jun 2020 20:08:36: Fewer paired peaks (120) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 120 pairs to build model! INFO @ Sun, 21 Jun 2020 20:08:36: start model_add_line... INFO @ Sun, 21 Jun 2020 20:08:37: start X-correlation... INFO @ Sun, 21 Jun 2020 20:08:37: end of X-cor INFO @ Sun, 21 Jun 2020 20:08:37: #2 finished! INFO @ Sun, 21 Jun 2020 20:08:37: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 20:08:37: #2 alternative fragment length(s) may be 2,45 bps INFO @ Sun, 21 Jun 2020 20:08:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3159494/SRX3159494.20_model.r WARNING @ Sun, 21 Jun 2020 20:08:37: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:08:37: #2 You may need to consider one of the other alternative d(s): 2,45 WARNING @ Sun, 21 Jun 2020 20:08:37: #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 20:08:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:08:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:08:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3159494/SRX3159494.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:08:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3159494/SRX3159494.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:08:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3159494/SRX3159494.05_summits.bed INFO @ Sun, 21 Jun 2020 20:08:53: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:09:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:09:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3159494/SRX3159494.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:09:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3159494/SRX3159494.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:09:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3159494/SRX3159494.10_summits.bed INFO @ Sun, 21 Jun 2020 20:09:24: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:09:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:09:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3159494/SRX3159494.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:09:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3159494/SRX3159494.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:09:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3159494/SRX3159494.20_summits.bed INFO @ Sun, 21 Jun 2020 20:09:53: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling