Job ID = 6453744 SRX = SRX1433390 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:38:09 prefetch.2.10.7: 1) Downloading 'SRR2919806'... 2020-06-21T08:38:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:42:57 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:42:57 prefetch.2.10.7: 1) 'SRR2919806' was downloaded successfully Read 43981994 spots for SRR2919806/SRR2919806.sra Written 43981994 spots for SRR2919806/SRR2919806.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: 00:00:01 Multiseed full-index search: 00:09:52 43981994 reads; of these: 43981994 (100.00%) were unpaired; of these: 1538177 (3.50%) aligned 0 times 31503231 (71.63%) aligned exactly 1 time 10940586 (24.88%) aligned >1 times 96.50% overall alignment rate Time searching: 00:09:53 Overall time: 00:09:53 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] 10561624 / 42443817 = 0.2488 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 18:02:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433390/SRX1433390.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433390/SRX1433390.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433390/SRX1433390.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433390/SRX1433390.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 18:02:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:02:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:02:16: 1000000 INFO @ Sun, 21 Jun 2020 18:02:21: 2000000 INFO @ Sun, 21 Jun 2020 18:02:26: 3000000 INFO @ Sun, 21 Jun 2020 18:02:30: 4000000 INFO @ Sun, 21 Jun 2020 18:02:35: 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 18:02:40: 6000000 INFO @ Sun, 21 Jun 2020 18:02:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433390/SRX1433390.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433390/SRX1433390.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433390/SRX1433390.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433390/SRX1433390.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 18:02:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:02:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:02:45: 7000000 INFO @ Sun, 21 Jun 2020 18:02:47: 1000000 INFO @ Sun, 21 Jun 2020 18:02:50: 8000000 INFO @ Sun, 21 Jun 2020 18:02:53: 2000000 INFO @ Sun, 21 Jun 2020 18:02:55: 9000000 INFO @ Sun, 21 Jun 2020 18:02:59: 3000000 INFO @ Sun, 21 Jun 2020 18:03:00: 10000000 INFO @ Sun, 21 Jun 2020 18:03:05: 4000000 INFO @ Sun, 21 Jun 2020 18:03:06: 11000000 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 18:03:11: 12000000 INFO @ Sun, 21 Jun 2020 18:03:11: 5000000 INFO @ Sun, 21 Jun 2020 18:03:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433390/SRX1433390.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433390/SRX1433390.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433390/SRX1433390.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433390/SRX1433390.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 18:03:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:03:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:03:16: 13000000 INFO @ Sun, 21 Jun 2020 18:03:16: 1000000 INFO @ Sun, 21 Jun 2020 18:03:17: 6000000 INFO @ Sun, 21 Jun 2020 18:03:21: 14000000 INFO @ Sun, 21 Jun 2020 18:03:22: 2000000 INFO @ Sun, 21 Jun 2020 18:03:23: 7000000 INFO @ Sun, 21 Jun 2020 18:03:26: 15000000 INFO @ Sun, 21 Jun 2020 18:03:27: 3000000 INFO @ Sun, 21 Jun 2020 18:03:29: 8000000 INFO @ Sun, 21 Jun 2020 18:03:32: 16000000 INFO @ Sun, 21 Jun 2020 18:03:32: 4000000 INFO @ Sun, 21 Jun 2020 18:03:35: 9000000 INFO @ Sun, 21 Jun 2020 18:03:37: 17000000 INFO @ Sun, 21 Jun 2020 18:03:37: 5000000 INFO @ Sun, 21 Jun 2020 18:03:41: 10000000 INFO @ Sun, 21 Jun 2020 18:03:42: 18000000 INFO @ Sun, 21 Jun 2020 18:03:42: 6000000 INFO @ Sun, 21 Jun 2020 18:03:47: 11000000 INFO @ Sun, 21 Jun 2020 18:03:47: 19000000 INFO @ Sun, 21 Jun 2020 18:03:48: 7000000 INFO @ Sun, 21 Jun 2020 18:03:53: 20000000 INFO @ Sun, 21 Jun 2020 18:03:53: 12000000 INFO @ Sun, 21 Jun 2020 18:03:53: 8000000 INFO @ Sun, 21 Jun 2020 18:03:58: 21000000 INFO @ Sun, 21 Jun 2020 18:03:58: 9000000 INFO @ Sun, 21 Jun 2020 18:03:59: 13000000 INFO @ Sun, 21 Jun 2020 18:04:03: 22000000 INFO @ Sun, 21 Jun 2020 18:04:03: 10000000 INFO @ Sun, 21 Jun 2020 18:04:05: 14000000 INFO @ Sun, 21 Jun 2020 18:04:08: 23000000 INFO @ Sun, 21 Jun 2020 18:04:09: 11000000 INFO @ Sun, 21 Jun 2020 18:04:11: 15000000 INFO @ Sun, 21 Jun 2020 18:04:14: 24000000 INFO @ Sun, 21 Jun 2020 18:04:14: 12000000 INFO @ Sun, 21 Jun 2020 18:04:17: 16000000 INFO @ Sun, 21 Jun 2020 18:04:19: 25000000 INFO @ Sun, 21 Jun 2020 18:04:19: 13000000 INFO @ Sun, 21 Jun 2020 18:04:23: 17000000 INFO @ Sun, 21 Jun 2020 18:04:24: 26000000 INFO @ Sun, 21 Jun 2020 18:04:24: 14000000 INFO @ Sun, 21 Jun 2020 18:04:29: 18000000 INFO @ Sun, 21 Jun 2020 18:04:29: 27000000 INFO @ Sun, 21 Jun 2020 18:04:30: 15000000 INFO @ Sun, 21 Jun 2020 18:04:35: 19000000 INFO @ Sun, 21 Jun 2020 18:04:35: 16000000 INFO @ Sun, 21 Jun 2020 18:04:35: 28000000 INFO @ Sun, 21 Jun 2020 18:04:40: 17000000 INFO @ Sun, 21 Jun 2020 18:04:40: 29000000 INFO @ Sun, 21 Jun 2020 18:04:41: 20000000 INFO @ Sun, 21 Jun 2020 18:04:45: 18000000 INFO @ Sun, 21 Jun 2020 18:04:46: 30000000 INFO @ Sun, 21 Jun 2020 18:04:47: 21000000 INFO @ Sun, 21 Jun 2020 18:04:50: 19000000 INFO @ Sun, 21 Jun 2020 18:04:51: 31000000 INFO @ Sun, 21 Jun 2020 18:04:53: 22000000 INFO @ Sun, 21 Jun 2020 18:04:56: 20000000 INFO @ Sun, 21 Jun 2020 18:04:56: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 18:04:56: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 18:04:56: #1 total tags in treatment: 31882193 INFO @ Sun, 21 Jun 2020 18:04:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:04:56: #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 18:04:57: #1 tags after filtering in treatment: 31882154 INFO @ Sun, 21 Jun 2020 18:04:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:04:57: #1 finished! INFO @ Sun, 21 Jun 2020 18:04:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:04:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:04:59: 23000000 INFO @ Sun, 21 Jun 2020 18:04:59: #2 number of paired peaks: 229 WARNING @ Sun, 21 Jun 2020 18:04:59: Fewer paired peaks (229) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 229 pairs to build model! INFO @ Sun, 21 Jun 2020 18:04:59: start model_add_line... INFO @ Sun, 21 Jun 2020 18:04:59: start X-correlation... INFO @ Sun, 21 Jun 2020 18:04:59: end of X-cor INFO @ Sun, 21 Jun 2020 18:04:59: #2 finished! INFO @ Sun, 21 Jun 2020 18:04:59: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 18:04:59: #2 alternative fragment length(s) may be 1,15,46 bps INFO @ Sun, 21 Jun 2020 18:04:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433390/SRX1433390.05_model.r WARNING @ Sun, 21 Jun 2020 18:04:59: #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 18:04:59: #2 You may need to consider one of the other alternative d(s): 1,15,46 WARNING @ Sun, 21 Jun 2020 18:04:59: #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 18:04:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:04:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:05:01: 21000000 INFO @ Sun, 21 Jun 2020 18:05:05: 24000000 INFO @ Sun, 21 Jun 2020 18:05:06: 22000000 INFO @ Sun, 21 Jun 2020 18:05:11: 25000000 INFO @ Sun, 21 Jun 2020 18:05:11: 23000000 INFO @ Sun, 21 Jun 2020 18:05:16: 26000000 INFO @ Sun, 21 Jun 2020 18:05:17: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:05:22: 25000000 INFO @ Sun, 21 Jun 2020 18:05:23: 27000000 INFO @ Sun, 21 Jun 2020 18:05:27: 26000000 INFO @ Sun, 21 Jun 2020 18:05:29: 28000000 INFO @ Sun, 21 Jun 2020 18:05:33: 27000000 INFO @ Sun, 21 Jun 2020 18:05:35: 29000000 INFO @ Sun, 21 Jun 2020 18:05:38: 28000000 INFO @ Sun, 21 Jun 2020 18:05:41: 30000000 INFO @ Sun, 21 Jun 2020 18:05:43: 29000000 INFO @ Sun, 21 Jun 2020 18:05:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:05:47: 31000000 INFO @ Sun, 21 Jun 2020 18:05:49: 30000000 INFO @ Sun, 21 Jun 2020 18:05:52: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 18:05:52: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 18:05:52: #1 total tags in treatment: 31882193 INFO @ Sun, 21 Jun 2020 18:05:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:05:52: #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 18:05:53: #1 tags after filtering in treatment: 31882154 INFO @ Sun, 21 Jun 2020 18:05:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:05:53: #1 finished! INFO @ Sun, 21 Jun 2020 18:05:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:05:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:05:54: 31000000 INFO @ Sun, 21 Jun 2020 18:05:55: #2 number of paired peaks: 229 WARNING @ Sun, 21 Jun 2020 18:05:55: Fewer paired peaks (229) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 229 pairs to build model! INFO @ Sun, 21 Jun 2020 18:05:55: start model_add_line... INFO @ Sun, 21 Jun 2020 18:05:55: start X-correlation... INFO @ Sun, 21 Jun 2020 18:05:55: end of X-cor INFO @ Sun, 21 Jun 2020 18:05:55: #2 finished! INFO @ Sun, 21 Jun 2020 18:05:55: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 18:05:55: #2 alternative fragment length(s) may be 1,15,46 bps INFO @ Sun, 21 Jun 2020 18:05:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433390/SRX1433390.10_model.r WARNING @ Sun, 21 Jun 2020 18:05:55: #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 18:05:55: #2 You may need to consider one of the other alternative d(s): 1,15,46 WARNING @ Sun, 21 Jun 2020 18:05:55: #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 18:05:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:05:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:05:59: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 18:05:59: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 18:05:59: #1 total tags in treatment: 31882193 INFO @ Sun, 21 Jun 2020 18:05:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:05:59: #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 18:05:59: #1 tags after filtering in treatment: 31882154 INFO @ Sun, 21 Jun 2020 18:05:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:05:59: #1 finished! INFO @ Sun, 21 Jun 2020 18:05:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:05:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:06:01: #2 number of paired peaks: 229 WARNING @ Sun, 21 Jun 2020 18:06:01: Fewer paired peaks (229) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 229 pairs to build model! INFO @ Sun, 21 Jun 2020 18:06:01: start model_add_line... INFO @ Sun, 21 Jun 2020 18:06:01: start X-correlation... INFO @ Sun, 21 Jun 2020 18:06:01: end of X-cor INFO @ Sun, 21 Jun 2020 18:06:01: #2 finished! INFO @ Sun, 21 Jun 2020 18:06:01: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 18:06:01: #2 alternative fragment length(s) may be 1,15,46 bps INFO @ Sun, 21 Jun 2020 18:06:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433390/SRX1433390.20_model.r WARNING @ Sun, 21 Jun 2020 18:06:01: #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 18:06:01: #2 You may need to consider one of the other alternative d(s): 1,15,46 WARNING @ Sun, 21 Jun 2020 18:06:01: #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 18:06:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:06:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:06:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433390/SRX1433390.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:06:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433390/SRX1433390.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:06:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433390/SRX1433390.05_summits.bed INFO @ Sun, 21 Jun 2020 18:06:08: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:06:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:06:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:07:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433390/SRX1433390.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:07:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433390/SRX1433390.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:07:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433390/SRX1433390.10_summits.bed INFO @ Sun, 21 Jun 2020 18:07:03: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:07:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433390/SRX1433390.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:07:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433390/SRX1433390.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:07:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433390/SRX1433390.20_summits.bed INFO @ Sun, 21 Jun 2020 18:07:10: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling