Job ID = 6454966 SRX = SRX2618509 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:34:10 prefetch.2.10.7: 1) Downloading 'SRR5319063'... 2020-06-21T09:34:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:39:41 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:39:41 prefetch.2.10.7: 1) 'SRR5319063' was downloaded successfully 2020-06-21T09:39:41 prefetch.2.10.7: 'SRR5319063' has 0 unresolved dependencies Read 45963706 spots for SRR5319063/SRR5319063.sra Written 45963706 spots for SRR5319063/SRR5319063.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: 00:09:22 45963706 reads; of these: 45963706 (100.00%) were unpaired; of these: 15314336 (33.32%) aligned 0 times 23628553 (51.41%) aligned exactly 1 time 7020817 (15.27%) aligned >1 times 66.68% overall alignment rate Time searching: 00:09:22 Overall time: 00:09:22 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] 4968283 / 30649370 = 0.1621 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 18:59:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618509/SRX2618509.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618509/SRX2618509.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618509/SRX2618509.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618509/SRX2618509.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 18:59:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:59:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:59:59: 1000000 INFO @ Sun, 21 Jun 2020 19:00:05: 2000000 INFO @ Sun, 21 Jun 2020 19:00:11: 3000000 INFO @ Sun, 21 Jun 2020 19:00:17: 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 19:00:22: 5000000 INFO @ Sun, 21 Jun 2020 19:00:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618509/SRX2618509.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618509/SRX2618509.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618509/SRX2618509.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618509/SRX2618509.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 19:00:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:00:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:00:28: 6000000 INFO @ Sun, 21 Jun 2020 19:00:30: 1000000 INFO @ Sun, 21 Jun 2020 19:00:35: 7000000 INFO @ Sun, 21 Jun 2020 19:00:36: 2000000 INFO @ Sun, 21 Jun 2020 19:00:41: 8000000 INFO @ Sun, 21 Jun 2020 19:00:42: 3000000 INFO @ Sun, 21 Jun 2020 19:00:47: 9000000 INFO @ Sun, 21 Jun 2020 19:00:48: 4000000 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 19:00:53: 10000000 INFO @ Sun, 21 Jun 2020 19:00:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618509/SRX2618509.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618509/SRX2618509.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618509/SRX2618509.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618509/SRX2618509.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 19:00:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:00:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:00:55: 5000000 INFO @ Sun, 21 Jun 2020 19:01:00: 11000000 INFO @ Sun, 21 Jun 2020 19:01:00: 1000000 INFO @ Sun, 21 Jun 2020 19:01:01: 6000000 INFO @ Sun, 21 Jun 2020 19:01:06: 12000000 INFO @ Sun, 21 Jun 2020 19:01:07: 2000000 INFO @ Sun, 21 Jun 2020 19:01:08: 7000000 INFO @ Sun, 21 Jun 2020 19:01:13: 13000000 INFO @ Sun, 21 Jun 2020 19:01:14: 3000000 INFO @ Sun, 21 Jun 2020 19:01:15: 8000000 INFO @ Sun, 21 Jun 2020 19:01:21: 4000000 INFO @ Sun, 21 Jun 2020 19:01:21: 14000000 INFO @ Sun, 21 Jun 2020 19:01:23: 9000000 INFO @ Sun, 21 Jun 2020 19:01:27: 5000000 INFO @ Sun, 21 Jun 2020 19:01:29: 15000000 INFO @ Sun, 21 Jun 2020 19:01:30: 10000000 INFO @ Sun, 21 Jun 2020 19:01:34: 6000000 INFO @ Sun, 21 Jun 2020 19:01:36: 16000000 INFO @ Sun, 21 Jun 2020 19:01:38: 11000000 INFO @ Sun, 21 Jun 2020 19:01:40: 7000000 INFO @ Sun, 21 Jun 2020 19:01:45: 17000000 INFO @ Sun, 21 Jun 2020 19:01:46: 12000000 INFO @ Sun, 21 Jun 2020 19:01:46: 8000000 INFO @ Sun, 21 Jun 2020 19:01:53: 9000000 INFO @ Sun, 21 Jun 2020 19:01:53: 18000000 INFO @ Sun, 21 Jun 2020 19:01:54: 13000000 INFO @ Sun, 21 Jun 2020 19:01:59: 10000000 INFO @ Sun, 21 Jun 2020 19:02:01: 19000000 INFO @ Sun, 21 Jun 2020 19:02:03: 14000000 INFO @ Sun, 21 Jun 2020 19:02:06: 11000000 INFO @ Sun, 21 Jun 2020 19:02:09: 20000000 INFO @ Sun, 21 Jun 2020 19:02:11: 15000000 INFO @ Sun, 21 Jun 2020 19:02:13: 12000000 INFO @ Sun, 21 Jun 2020 19:02:19: 21000000 INFO @ Sun, 21 Jun 2020 19:02:19: 16000000 INFO @ Sun, 21 Jun 2020 19:02:20: 13000000 INFO @ Sun, 21 Jun 2020 19:02:27: 22000000 INFO @ Sun, 21 Jun 2020 19:02:27: 14000000 INFO @ Sun, 21 Jun 2020 19:02:28: 17000000 INFO @ Sun, 21 Jun 2020 19:02:34: 15000000 INFO @ Sun, 21 Jun 2020 19:02:35: 23000000 INFO @ Sun, 21 Jun 2020 19:02:36: 18000000 INFO @ Sun, 21 Jun 2020 19:02:41: 16000000 INFO @ Sun, 21 Jun 2020 19:02:44: 24000000 INFO @ Sun, 21 Jun 2020 19:02:45: 19000000 INFO @ Sun, 21 Jun 2020 19:02:47: 17000000 INFO @ Sun, 21 Jun 2020 19:02:53: 25000000 INFO @ Sun, 21 Jun 2020 19:02:53: 20000000 INFO @ Sun, 21 Jun 2020 19:02:54: 18000000 INFO @ Sun, 21 Jun 2020 19:02:59: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:02:59: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:02:59: #1 total tags in treatment: 25681087 INFO @ Sun, 21 Jun 2020 19:02:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:02:59: #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 19:03:00: #1 tags after filtering in treatment: 25681087 INFO @ Sun, 21 Jun 2020 19:03:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:03:00: #1 finished! INFO @ Sun, 21 Jun 2020 19:03:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:03:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:03:01: 19000000 INFO @ Sun, 21 Jun 2020 19:03:01: #2 number of paired peaks: 573 WARNING @ Sun, 21 Jun 2020 19:03:01: Fewer paired peaks (573) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 573 pairs to build model! INFO @ Sun, 21 Jun 2020 19:03:01: start model_add_line... INFO @ Sun, 21 Jun 2020 19:03:02: start X-correlation... INFO @ Sun, 21 Jun 2020 19:03:02: end of X-cor INFO @ Sun, 21 Jun 2020 19:03:02: #2 finished! INFO @ Sun, 21 Jun 2020 19:03:02: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 19:03:02: #2 alternative fragment length(s) may be 2,588,591 bps INFO @ Sun, 21 Jun 2020 19:03:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618509/SRX2618509.05_model.r WARNING @ Sun, 21 Jun 2020 19:03:02: #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 19:03:02: #2 You may need to consider one of the other alternative d(s): 2,588,591 WARNING @ Sun, 21 Jun 2020 19:03:02: #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 19:03:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:03:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:03:02: 21000000 INFO @ Sun, 21 Jun 2020 19:03:07: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:03:11: 22000000 INFO @ Sun, 21 Jun 2020 19:03:15: 21000000 INFO @ Sun, 21 Jun 2020 19:03:19: 23000000 INFO @ Sun, 21 Jun 2020 19:03:21: 22000000 INFO @ Sun, 21 Jun 2020 19:03:27: 24000000 INFO @ Sun, 21 Jun 2020 19:03:28: 23000000 INFO @ Sun, 21 Jun 2020 19:03:35: 24000000 INFO @ Sun, 21 Jun 2020 19:03:35: 25000000 INFO @ Sun, 21 Jun 2020 19:03:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:03:41: 25000000 INFO @ Sun, 21 Jun 2020 19:03:41: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:03:41: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:03:41: #1 total tags in treatment: 25681087 INFO @ Sun, 21 Jun 2020 19:03:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:03:41: #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 19:03:42: #1 tags after filtering in treatment: 25681087 INFO @ Sun, 21 Jun 2020 19:03:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:03:42: #1 finished! INFO @ Sun, 21 Jun 2020 19:03:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:03:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:03:44: #2 number of paired peaks: 573 WARNING @ Sun, 21 Jun 2020 19:03:44: Fewer paired peaks (573) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 573 pairs to build model! INFO @ Sun, 21 Jun 2020 19:03:44: start model_add_line... INFO @ Sun, 21 Jun 2020 19:03:44: start X-correlation... INFO @ Sun, 21 Jun 2020 19:03:44: end of X-cor INFO @ Sun, 21 Jun 2020 19:03:44: #2 finished! INFO @ Sun, 21 Jun 2020 19:03:44: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 19:03:44: #2 alternative fragment length(s) may be 2,588,591 bps INFO @ Sun, 21 Jun 2020 19:03:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618509/SRX2618509.10_model.r WARNING @ Sun, 21 Jun 2020 19:03:44: #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 19:03:44: #2 You may need to consider one of the other alternative d(s): 2,588,591 WARNING @ Sun, 21 Jun 2020 19:03:44: #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 19:03:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:03:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:03:46: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:03:46: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:03:46: #1 total tags in treatment: 25681087 INFO @ Sun, 21 Jun 2020 19:03:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:03:46: #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 19:03:47: #1 tags after filtering in treatment: 25681087 INFO @ Sun, 21 Jun 2020 19:03:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:03:47: #1 finished! INFO @ Sun, 21 Jun 2020 19:03:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:03:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:03:49: #2 number of paired peaks: 573 WARNING @ Sun, 21 Jun 2020 19:03:49: Fewer paired peaks (573) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 573 pairs to build model! INFO @ Sun, 21 Jun 2020 19:03:49: start model_add_line... INFO @ Sun, 21 Jun 2020 19:03:49: start X-correlation... INFO @ Sun, 21 Jun 2020 19:03:49: end of X-cor INFO @ Sun, 21 Jun 2020 19:03:49: #2 finished! INFO @ Sun, 21 Jun 2020 19:03:49: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 19:03:49: #2 alternative fragment length(s) may be 2,588,591 bps INFO @ Sun, 21 Jun 2020 19:03:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618509/SRX2618509.20_model.r WARNING @ Sun, 21 Jun 2020 19:03:49: #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 19:03:49: #2 You may need to consider one of the other alternative d(s): 2,588,591 WARNING @ Sun, 21 Jun 2020 19:03:49: #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 19:03:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:03:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:03:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618509/SRX2618509.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:03:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618509/SRX2618509.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:03:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618509/SRX2618509.05_summits.bed INFO @ Sun, 21 Jun 2020 19:03:58: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:04:22: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:04:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:04:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618509/SRX2618509.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:04:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618509/SRX2618509.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:04:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618509/SRX2618509.10_summits.bed INFO @ Sun, 21 Jun 2020 19:04:40: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:04:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618509/SRX2618509.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:04:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618509/SRX2618509.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:04:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618509/SRX2618509.20_summits.bed INFO @ Sun, 21 Jun 2020 19:04:45: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling