Job ID = 6456746 SRX = SRX3981646 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:58:31 prefetch.2.10.7: 1) Downloading 'SRR7050322'... 2020-06-21T10:58:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:01:04 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:01:04 prefetch.2.10.7: 'SRR7050322' is valid 2020-06-21T11:01:04 prefetch.2.10.7: 1) 'SRR7050322' was downloaded successfully 2020-06-21T11:01:04 prefetch.2.10.7: 'SRR7050322' has 0 unresolved dependencies Read 14650562 spots for SRR7050322/SRR7050322.sra Written 14650562 spots for SRR7050322/SRR7050322.sra 2020-06-21T11:01:59 prefetch.2.10.7: 1) Downloading 'SRR7050323'... 2020-06-21T11:01:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:03:42 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:03:42 prefetch.2.10.7: 'SRR7050323' is valid 2020-06-21T11:03:42 prefetch.2.10.7: 1) 'SRR7050323' was downloaded successfully 2020-06-21T11:03:42 prefetch.2.10.7: 'SRR7050323' has 0 unresolved dependencies Read 14538813 spots for SRR7050323/SRR7050323.sra Written 14538813 spots for SRR7050323/SRR7050323.sra 2020-06-21T11:04:37 prefetch.2.10.7: 1) Downloading 'SRR7050324'... 2020-06-21T11:04:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:06:06 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:06:06 prefetch.2.10.7: 'SRR7050324' is valid 2020-06-21T11:06:06 prefetch.2.10.7: 1) 'SRR7050324' was downloaded successfully 2020-06-21T11:06:06 prefetch.2.10.7: 'SRR7050324' has 0 unresolved dependencies Read 14521715 spots for SRR7050324/SRR7050324.sra Written 14521715 spots for SRR7050324/SRR7050324.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: 00:10:06 43711090 reads; of these: 43711090 (100.00%) were unpaired; of these: 1594386 (3.65%) aligned 0 times 35553241 (81.34%) aligned exactly 1 time 6563463 (15.02%) aligned >1 times 96.35% overall alignment rate Time searching: 00:10:06 Overall time: 00:10:06 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] 9192354 / 42116704 = 0.2183 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 20:25:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981646/SRX3981646.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981646/SRX3981646.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981646/SRX3981646.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981646/SRX3981646.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 20:25:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:25:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:25:53: 1000000 INFO @ Sun, 21 Jun 2020 20:25:58: 2000000 INFO @ Sun, 21 Jun 2020 20:26:03: 3000000 INFO @ Sun, 21 Jun 2020 20:26:09: 4000000 INFO @ Sun, 21 Jun 2020 20:26:14: 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 20:26:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981646/SRX3981646.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981646/SRX3981646.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981646/SRX3981646.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981646/SRX3981646.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 20:26:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:26:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:26:19: 6000000 INFO @ Sun, 21 Jun 2020 20:26:24: 1000000 INFO @ Sun, 21 Jun 2020 20:26:25: 7000000 INFO @ Sun, 21 Jun 2020 20:26:30: 2000000 INFO @ Sun, 21 Jun 2020 20:26:30: 8000000 INFO @ Sun, 21 Jun 2020 20:26:35: 3000000 INFO @ Sun, 21 Jun 2020 20:26:36: 9000000 INFO @ Sun, 21 Jun 2020 20:26:41: 4000000 INFO @ Sun, 21 Jun 2020 20:26:42: 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 20:26:47: 5000000 INFO @ Sun, 21 Jun 2020 20:26:47: 11000000 INFO @ Sun, 21 Jun 2020 20:26:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981646/SRX3981646.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981646/SRX3981646.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981646/SRX3981646.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981646/SRX3981646.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 20:26:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:26:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:26:53: 6000000 INFO @ Sun, 21 Jun 2020 20:26:53: 12000000 INFO @ Sun, 21 Jun 2020 20:26:54: 1000000 INFO @ Sun, 21 Jun 2020 20:26:59: 7000000 INFO @ Sun, 21 Jun 2020 20:26:59: 13000000 INFO @ Sun, 21 Jun 2020 20:26:59: 2000000 INFO @ Sun, 21 Jun 2020 20:27:05: 14000000 INFO @ Sun, 21 Jun 2020 20:27:05: 8000000 INFO @ Sun, 21 Jun 2020 20:27:05: 3000000 INFO @ Sun, 21 Jun 2020 20:27:11: 15000000 INFO @ Sun, 21 Jun 2020 20:27:11: 9000000 INFO @ Sun, 21 Jun 2020 20:27:11: 4000000 INFO @ Sun, 21 Jun 2020 20:27:16: 16000000 INFO @ Sun, 21 Jun 2020 20:27:16: 10000000 INFO @ Sun, 21 Jun 2020 20:27:17: 5000000 INFO @ Sun, 21 Jun 2020 20:27:22: 17000000 INFO @ Sun, 21 Jun 2020 20:27:22: 11000000 INFO @ Sun, 21 Jun 2020 20:27:23: 6000000 INFO @ Sun, 21 Jun 2020 20:27:28: 18000000 INFO @ Sun, 21 Jun 2020 20:27:28: 12000000 INFO @ Sun, 21 Jun 2020 20:27:28: 7000000 INFO @ Sun, 21 Jun 2020 20:27:34: 19000000 INFO @ Sun, 21 Jun 2020 20:27:34: 13000000 INFO @ Sun, 21 Jun 2020 20:27:34: 8000000 INFO @ Sun, 21 Jun 2020 20:27:40: 20000000 INFO @ Sun, 21 Jun 2020 20:27:40: 14000000 INFO @ Sun, 21 Jun 2020 20:27:40: 9000000 INFO @ Sun, 21 Jun 2020 20:27:46: 21000000 INFO @ Sun, 21 Jun 2020 20:27:46: 10000000 INFO @ Sun, 21 Jun 2020 20:27:46: 15000000 INFO @ Sun, 21 Jun 2020 20:27:52: 22000000 INFO @ Sun, 21 Jun 2020 20:27:52: 11000000 INFO @ Sun, 21 Jun 2020 20:27:52: 16000000 INFO @ Sun, 21 Jun 2020 20:27:57: 12000000 INFO @ Sun, 21 Jun 2020 20:27:57: 23000000 INFO @ Sun, 21 Jun 2020 20:27:58: 17000000 INFO @ Sun, 21 Jun 2020 20:28:03: 13000000 INFO @ Sun, 21 Jun 2020 20:28:03: 24000000 INFO @ Sun, 21 Jun 2020 20:28:04: 18000000 INFO @ Sun, 21 Jun 2020 20:28:09: 14000000 INFO @ Sun, 21 Jun 2020 20:28:09: 25000000 INFO @ Sun, 21 Jun 2020 20:28:10: 19000000 INFO @ Sun, 21 Jun 2020 20:28:15: 15000000 INFO @ Sun, 21 Jun 2020 20:28:15: 26000000 INFO @ Sun, 21 Jun 2020 20:28:16: 20000000 INFO @ Sun, 21 Jun 2020 20:28:21: 16000000 INFO @ Sun, 21 Jun 2020 20:28:21: 27000000 INFO @ Sun, 21 Jun 2020 20:28:21: 21000000 INFO @ Sun, 21 Jun 2020 20:28:27: 17000000 INFO @ Sun, 21 Jun 2020 20:28:27: 28000000 INFO @ Sun, 21 Jun 2020 20:28:27: 22000000 INFO @ Sun, 21 Jun 2020 20:28:32: 18000000 INFO @ Sun, 21 Jun 2020 20:28:33: 29000000 INFO @ Sun, 21 Jun 2020 20:28:33: 23000000 INFO @ Sun, 21 Jun 2020 20:28:38: 19000000 INFO @ Sun, 21 Jun 2020 20:28:39: 30000000 INFO @ Sun, 21 Jun 2020 20:28:39: 24000000 INFO @ Sun, 21 Jun 2020 20:28:44: 20000000 INFO @ Sun, 21 Jun 2020 20:28:45: 31000000 INFO @ Sun, 21 Jun 2020 20:28:45: 25000000 INFO @ Sun, 21 Jun 2020 20:28:50: 21000000 INFO @ Sun, 21 Jun 2020 20:28:51: 32000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:28:51: 26000000 INFO @ Sun, 21 Jun 2020 20:28:56: 22000000 INFO @ Sun, 21 Jun 2020 20:28:56: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:28:56: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:28:56: #1 total tags in treatment: 32924350 INFO @ Sun, 21 Jun 2020 20:28:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:28:56: #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 20:28:57: #1 tags after filtering in treatment: 32924284 INFO @ Sun, 21 Jun 2020 20:28:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:28:57: #1 finished! INFO @ Sun, 21 Jun 2020 20:28:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:28:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:28:57: 27000000 INFO @ Sun, 21 Jun 2020 20:28:59: #2 number of paired peaks: 541 WARNING @ Sun, 21 Jun 2020 20:28:59: Fewer paired peaks (541) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 541 pairs to build model! INFO @ Sun, 21 Jun 2020 20:28:59: start model_add_line... INFO @ Sun, 21 Jun 2020 20:28:59: start X-correlation... INFO @ Sun, 21 Jun 2020 20:28:59: end of X-cor INFO @ Sun, 21 Jun 2020 20:28:59: #2 finished! INFO @ Sun, 21 Jun 2020 20:28:59: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 20:28:59: #2 alternative fragment length(s) may be 1,51,68,84,157,162 bps INFO @ Sun, 21 Jun 2020 20:28:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981646/SRX3981646.05_model.r WARNING @ Sun, 21 Jun 2020 20:28:59: #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 20:28:59: #2 You may need to consider one of the other alternative d(s): 1,51,68,84,157,162 WARNING @ Sun, 21 Jun 2020 20:28:59: #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 20:28:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:28:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:29:02: 23000000 INFO @ Sun, 21 Jun 2020 20:29:03: 28000000 INFO @ Sun, 21 Jun 2020 20:29:08: 24000000 INFO @ Sun, 21 Jun 2020 20:29:09: 29000000 INFO @ Sun, 21 Jun 2020 20:29:14: 25000000 INFO @ Sun, 21 Jun 2020 20:29:16: 30000000 INFO @ Sun, 21 Jun 2020 20:29:20: 26000000 INFO @ Sun, 21 Jun 2020 20:29:22: 31000000 INFO @ Sun, 21 Jun 2020 20:29:26: 27000000 INFO @ Sun, 21 Jun 2020 20:29:27: 32000000 INFO @ Sun, 21 Jun 2020 20:29:32: 28000000 INFO @ Sun, 21 Jun 2020 20:29:33: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:29:33: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:29:33: #1 total tags in treatment: 32924350 INFO @ Sun, 21 Jun 2020 20:29:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:29:33: #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 20:29:34: #1 tags after filtering in treatment: 32924284 INFO @ Sun, 21 Jun 2020 20:29:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:29:34: #1 finished! INFO @ Sun, 21 Jun 2020 20:29:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:29:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:29:36: #2 number of paired peaks: 541 WARNING @ Sun, 21 Jun 2020 20:29:36: Fewer paired peaks (541) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 541 pairs to build model! INFO @ Sun, 21 Jun 2020 20:29:36: start model_add_line... INFO @ Sun, 21 Jun 2020 20:29:36: start X-correlation... INFO @ Sun, 21 Jun 2020 20:29:36: end of X-cor INFO @ Sun, 21 Jun 2020 20:29:36: #2 finished! INFO @ Sun, 21 Jun 2020 20:29:36: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 20:29:36: #2 alternative fragment length(s) may be 1,51,68,84,157,162 bps INFO @ Sun, 21 Jun 2020 20:29:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981646/SRX3981646.10_model.r WARNING @ Sun, 21 Jun 2020 20:29:36: #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 20:29:36: #2 You may need to consider one of the other alternative d(s): 1,51,68,84,157,162 WARNING @ Sun, 21 Jun 2020 20:29:36: #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 20:29:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:29:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:29:37: 29000000 INFO @ Sun, 21 Jun 2020 20:29:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:29:43: 30000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:29:48: 31000000 INFO @ Sun, 21 Jun 2020 20:29:54: 32000000 INFO @ Sun, 21 Jun 2020 20:29:59: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:29:59: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:29:59: #1 total tags in treatment: 32924350 INFO @ Sun, 21 Jun 2020 20:29:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:29:59: #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 20:30:00: #1 tags after filtering in treatment: 32924284 INFO @ Sun, 21 Jun 2020 20:30:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:30:00: #1 finished! INFO @ Sun, 21 Jun 2020 20:30:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:30:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:30:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981646/SRX3981646.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:30:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981646/SRX3981646.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:30:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981646/SRX3981646.05_summits.bed INFO @ Sun, 21 Jun 2020 20:30:02: Done! INFO @ Sun, 21 Jun 2020 20:30:02: #2 number of paired peaks: 541 WARNING @ Sun, 21 Jun 2020 20:30:02: Fewer paired peaks (541) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 541 pairs to build model! INFO @ Sun, 21 Jun 2020 20:30:02: start model_add_line... INFO @ Sun, 21 Jun 2020 20:30:02: start X-correlation... pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:30:02: end of X-cor INFO @ Sun, 21 Jun 2020 20:30:02: #2 finished! INFO @ Sun, 21 Jun 2020 20:30:02: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 20:30:02: #2 alternative fragment length(s) may be 1,51,68,84,157,162 bps INFO @ Sun, 21 Jun 2020 20:30:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981646/SRX3981646.20_model.r WARNING @ Sun, 21 Jun 2020 20:30:02: #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 20:30:02: #2 You may need to consider one of the other alternative d(s): 1,51,68,84,157,162 WARNING @ Sun, 21 Jun 2020 20:30:02: #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 20:30:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:30:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:30:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:30:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981646/SRX3981646.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:30:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981646/SRX3981646.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:30:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981646/SRX3981646.10_summits.bed INFO @ Sun, 21 Jun 2020 20:30:39: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:30:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:31:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981646/SRX3981646.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:31:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981646/SRX3981646.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:31:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981646/SRX3981646.20_summits.bed INFO @ Sun, 21 Jun 2020 20:31:03: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling