Job ID = 6458788 SRX = SRX5436061 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:37:56 prefetch.2.10.7: 1) Downloading 'SRR8637393'... 2020-06-21T12:37:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:41:44 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:41:44 prefetch.2.10.7: 1) 'SRR8637393' was downloaded successfully Read 45774333 spots for SRR8637393/SRR8637393.sra Written 45774333 spots for SRR8637393/SRR8637393.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: 00:12:18 45774333 reads; of these: 45774333 (100.00%) were unpaired; of these: 2306621 (5.04%) aligned 0 times 31066841 (67.87%) aligned exactly 1 time 12400871 (27.09%) aligned >1 times 94.96% overall alignment rate Time searching: 00:12:19 Overall time: 00:12:20 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] 9101430 / 43467712 = 0.2094 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 22:05:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5436061/SRX5436061.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5436061/SRX5436061.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5436061/SRX5436061.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5436061/SRX5436061.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 22:05:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:05:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:05:31: 1000000 INFO @ Sun, 21 Jun 2020 22:05:38: 2000000 INFO @ Sun, 21 Jun 2020 22:05:46: 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 22:05:53: 4000000 INFO @ Sun, 21 Jun 2020 22:05:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5436061/SRX5436061.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5436061/SRX5436061.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5436061/SRX5436061.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5436061/SRX5436061.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 22:05:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:05:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:06:01: 5000000 INFO @ Sun, 21 Jun 2020 22:06:02: 1000000 INFO @ Sun, 21 Jun 2020 22:06:09: 6000000 INFO @ Sun, 21 Jun 2020 22:06:10: 2000000 INFO @ Sun, 21 Jun 2020 22:06:17: 7000000 INFO @ Sun, 21 Jun 2020 22:06:18: 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 22:06:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5436061/SRX5436061.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5436061/SRX5436061.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5436061/SRX5436061.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5436061/SRX5436061.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 22:06:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:06:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:06:25: 8000000 INFO @ Sun, 21 Jun 2020 22:06:27: 4000000 INFO @ Sun, 21 Jun 2020 22:06:32: 1000000 INFO @ Sun, 21 Jun 2020 22:06:33: 9000000 INFO @ Sun, 21 Jun 2020 22:06:35: 5000000 INFO @ Sun, 21 Jun 2020 22:06:40: 2000000 INFO @ Sun, 21 Jun 2020 22:06:42: 10000000 INFO @ Sun, 21 Jun 2020 22:06:43: 6000000 INFO @ Sun, 21 Jun 2020 22:06:48: 3000000 INFO @ Sun, 21 Jun 2020 22:06:50: 11000000 INFO @ Sun, 21 Jun 2020 22:06:51: 7000000 INFO @ Sun, 21 Jun 2020 22:06:57: 4000000 INFO @ Sun, 21 Jun 2020 22:06:58: 12000000 INFO @ Sun, 21 Jun 2020 22:06:59: 8000000 INFO @ Sun, 21 Jun 2020 22:07:05: 5000000 INFO @ Sun, 21 Jun 2020 22:07:06: 13000000 INFO @ Sun, 21 Jun 2020 22:07:07: 9000000 INFO @ Sun, 21 Jun 2020 22:07:13: 6000000 INFO @ Sun, 21 Jun 2020 22:07:14: 14000000 INFO @ Sun, 21 Jun 2020 22:07:15: 10000000 INFO @ Sun, 21 Jun 2020 22:07:21: 7000000 INFO @ Sun, 21 Jun 2020 22:07:22: 15000000 INFO @ Sun, 21 Jun 2020 22:07:23: 11000000 INFO @ Sun, 21 Jun 2020 22:07:29: 8000000 INFO @ Sun, 21 Jun 2020 22:07:31: 16000000 INFO @ Sun, 21 Jun 2020 22:07:31: 12000000 INFO @ Sun, 21 Jun 2020 22:07:37: 9000000 INFO @ Sun, 21 Jun 2020 22:07:39: 13000000 INFO @ Sun, 21 Jun 2020 22:07:39: 17000000 INFO @ Sun, 21 Jun 2020 22:07:45: 10000000 INFO @ Sun, 21 Jun 2020 22:07:47: 14000000 INFO @ Sun, 21 Jun 2020 22:07:47: 18000000 INFO @ Sun, 21 Jun 2020 22:07:53: 11000000 INFO @ Sun, 21 Jun 2020 22:07:55: 15000000 INFO @ Sun, 21 Jun 2020 22:07:55: 19000000 INFO @ Sun, 21 Jun 2020 22:08:01: 12000000 INFO @ Sun, 21 Jun 2020 22:08:03: 16000000 INFO @ Sun, 21 Jun 2020 22:08:03: 20000000 INFO @ Sun, 21 Jun 2020 22:08:09: 13000000 INFO @ Sun, 21 Jun 2020 22:08:11: 17000000 INFO @ Sun, 21 Jun 2020 22:08:11: 21000000 INFO @ Sun, 21 Jun 2020 22:08:16: 14000000 INFO @ Sun, 21 Jun 2020 22:08:18: 18000000 INFO @ Sun, 21 Jun 2020 22:08:20: 22000000 INFO @ Sun, 21 Jun 2020 22:08:24: 15000000 INFO @ Sun, 21 Jun 2020 22:08:26: 19000000 INFO @ Sun, 21 Jun 2020 22:08:28: 23000000 INFO @ Sun, 21 Jun 2020 22:08:32: 16000000 INFO @ Sun, 21 Jun 2020 22:08:34: 20000000 INFO @ Sun, 21 Jun 2020 22:08:36: 24000000 INFO @ Sun, 21 Jun 2020 22:08:40: 17000000 INFO @ Sun, 21 Jun 2020 22:08:42: 21000000 INFO @ Sun, 21 Jun 2020 22:08:44: 25000000 INFO @ Sun, 21 Jun 2020 22:08:48: 18000000 INFO @ Sun, 21 Jun 2020 22:08:50: 22000000 INFO @ Sun, 21 Jun 2020 22:08:52: 26000000 INFO @ Sun, 21 Jun 2020 22:08:56: 19000000 INFO @ Sun, 21 Jun 2020 22:08:58: 23000000 INFO @ Sun, 21 Jun 2020 22:09:00: 27000000 INFO @ Sun, 21 Jun 2020 22:09:04: 20000000 INFO @ Sun, 21 Jun 2020 22:09:06: 24000000 INFO @ Sun, 21 Jun 2020 22:09:08: 28000000 INFO @ Sun, 21 Jun 2020 22:09:11: 21000000 INFO @ Sun, 21 Jun 2020 22:09:14: 25000000 INFO @ Sun, 21 Jun 2020 22:09:16: 29000000 INFO @ Sun, 21 Jun 2020 22:09:19: 22000000 INFO @ Sun, 21 Jun 2020 22:09:22: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:09:24: 30000000 INFO @ Sun, 21 Jun 2020 22:09:27: 23000000 INFO @ Sun, 21 Jun 2020 22:09:29: 27000000 INFO @ Sun, 21 Jun 2020 22:09:32: 31000000 INFO @ Sun, 21 Jun 2020 22:09:35: 24000000 INFO @ Sun, 21 Jun 2020 22:09:37: 28000000 INFO @ Sun, 21 Jun 2020 22:09:40: 32000000 INFO @ Sun, 21 Jun 2020 22:09:42: 25000000 INFO @ Sun, 21 Jun 2020 22:09:46: 29000000 INFO @ Sun, 21 Jun 2020 22:09:47: 33000000 INFO @ Sun, 21 Jun 2020 22:09:50: 26000000 INFO @ Sun, 21 Jun 2020 22:09:53: 30000000 INFO @ Sun, 21 Jun 2020 22:09:56: 34000000 INFO @ Sun, 21 Jun 2020 22:09:58: 27000000 INFO @ Sun, 21 Jun 2020 22:09:59: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:09:59: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:09:59: #1 total tags in treatment: 34366282 INFO @ Sun, 21 Jun 2020 22:09:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:09:59: #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 22:09:59: #1 tags after filtering in treatment: 34366220 INFO @ Sun, 21 Jun 2020 22:09:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:09:59: #1 finished! INFO @ Sun, 21 Jun 2020 22:09:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:09:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:10:01: 31000000 INFO @ Sun, 21 Jun 2020 22:10:02: #2 number of paired peaks: 422 WARNING @ Sun, 21 Jun 2020 22:10:02: Fewer paired peaks (422) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 422 pairs to build model! INFO @ Sun, 21 Jun 2020 22:10:02: start model_add_line... INFO @ Sun, 21 Jun 2020 22:10:02: start X-correlation... INFO @ Sun, 21 Jun 2020 22:10:02: end of X-cor INFO @ Sun, 21 Jun 2020 22:10:02: #2 finished! INFO @ Sun, 21 Jun 2020 22:10:02: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 22:10:02: #2 alternative fragment length(s) may be 1,31,45,585 bps INFO @ Sun, 21 Jun 2020 22:10:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5436061/SRX5436061.05_model.r WARNING @ Sun, 21 Jun 2020 22:10:02: #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 22:10:02: #2 You may need to consider one of the other alternative d(s): 1,31,45,585 WARNING @ Sun, 21 Jun 2020 22:10:02: #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 22:10:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:10:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:10:06: 28000000 INFO @ Sun, 21 Jun 2020 22:10:09: 32000000 INFO @ Sun, 21 Jun 2020 22:10:14: 29000000 INFO @ Sun, 21 Jun 2020 22:10:16: 33000000 INFO @ Sun, 21 Jun 2020 22:10:22: 30000000 INFO @ Sun, 21 Jun 2020 22:10:24: 34000000 INFO @ Sun, 21 Jun 2020 22:10:27: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:10:27: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:10:27: #1 total tags in treatment: 34366282 INFO @ Sun, 21 Jun 2020 22:10:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:10:27: #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 22:10:28: #1 tags after filtering in treatment: 34366220 INFO @ Sun, 21 Jun 2020 22:10:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:10:28: #1 finished! INFO @ Sun, 21 Jun 2020 22:10:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:10:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:10:29: 31000000 INFO @ Sun, 21 Jun 2020 22:10:30: #2 number of paired peaks: 422 WARNING @ Sun, 21 Jun 2020 22:10:30: Fewer paired peaks (422) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 422 pairs to build model! INFO @ Sun, 21 Jun 2020 22:10:30: start model_add_line... INFO @ Sun, 21 Jun 2020 22:10:30: start X-correlation... INFO @ Sun, 21 Jun 2020 22:10:31: end of X-cor INFO @ Sun, 21 Jun 2020 22:10:31: #2 finished! INFO @ Sun, 21 Jun 2020 22:10:31: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 22:10:31: #2 alternative fragment length(s) may be 1,31,45,585 bps INFO @ Sun, 21 Jun 2020 22:10:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5436061/SRX5436061.10_model.r WARNING @ Sun, 21 Jun 2020 22:10:31: #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 22:10:31: #2 You may need to consider one of the other alternative d(s): 1,31,45,585 WARNING @ Sun, 21 Jun 2020 22:10:31: #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 22:10:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:10:31: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:10:36: 32000000 INFO @ Sun, 21 Jun 2020 22:10:43: 33000000 INFO @ Sun, 21 Jun 2020 22:10:51: 34000000 INFO @ Sun, 21 Jun 2020 22:10:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:10:53: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:10:53: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:10:53: #1 total tags in treatment: 34366282 INFO @ Sun, 21 Jun 2020 22:10:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:10:53: #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 22:10:54: #1 tags after filtering in treatment: 34366220 INFO @ Sun, 21 Jun 2020 22:10:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:10:54: #1 finished! INFO @ Sun, 21 Jun 2020 22:10:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:10:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:10:56: #2 number of paired peaks: 422 WARNING @ Sun, 21 Jun 2020 22:10:56: Fewer paired peaks (422) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 422 pairs to build model! INFO @ Sun, 21 Jun 2020 22:10:56: start model_add_line... INFO @ Sun, 21 Jun 2020 22:10:57: start X-correlation... INFO @ Sun, 21 Jun 2020 22:10:57: end of X-cor INFO @ Sun, 21 Jun 2020 22:10:57: #2 finished! INFO @ Sun, 21 Jun 2020 22:10:57: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 22:10:57: #2 alternative fragment length(s) may be 1,31,45,585 bps INFO @ Sun, 21 Jun 2020 22:10:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5436061/SRX5436061.20_model.r WARNING @ Sun, 21 Jun 2020 22:10:57: #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 22:10:57: #2 You may need to consider one of the other alternative d(s): 1,31,45,585 WARNING @ Sun, 21 Jun 2020 22:10:57: #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 22:10:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:10:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:11:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5436061/SRX5436061.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:11:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5436061/SRX5436061.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:11:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5436061/SRX5436061.05_summits.bed INFO @ Sun, 21 Jun 2020 22:11:16: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:11:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:11:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5436061/SRX5436061.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:11:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5436061/SRX5436061.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:11:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5436061/SRX5436061.10_summits.bed INFO @ Sun, 21 Jun 2020 22:11:43: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:11:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:12:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5436061/SRX5436061.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:12:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5436061/SRX5436061.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:12:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5436061/SRX5436061.20_summits.bed INFO @ Sun, 21 Jun 2020 22:12:10: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling