Job ID = 6456757 SRX = SRX3981655 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:22:54 prefetch.2.10.7: 1) Downloading 'SRR7050349'... 2020-06-21T11:22:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:24:13 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:24:13 prefetch.2.10.7: 'SRR7050349' is valid 2020-06-21T11:24:13 prefetch.2.10.7: 1) 'SRR7050349' was downloaded successfully 2020-06-21T11:24:13 prefetch.2.10.7: 'SRR7050349' has 0 unresolved dependencies Read 11404344 spots for SRR7050349/SRR7050349.sra Written 11404344 spots for SRR7050349/SRR7050349.sra 2020-06-21T11:25:01 prefetch.2.10.7: 1) Downloading 'SRR7050350'... 2020-06-21T11:25:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:26:21 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:26:21 prefetch.2.10.7: 'SRR7050350' is valid 2020-06-21T11:26:21 prefetch.2.10.7: 1) 'SRR7050350' was downloaded successfully 2020-06-21T11:26:21 prefetch.2.10.7: 'SRR7050350' has 0 unresolved dependencies Read 11369091 spots for SRR7050350/SRR7050350.sra Written 11369091 spots for SRR7050350/SRR7050350.sra 2020-06-21T11:27:08 prefetch.2.10.7: 1) Downloading 'SRR7050351'... 2020-06-21T11:27:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:28:23 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:28:24 prefetch.2.10.7: 'SRR7050351' is valid 2020-06-21T11:28:24 prefetch.2.10.7: 1) 'SRR7050351' was downloaded successfully 2020-06-21T11:28:24 prefetch.2.10.7: 'SRR7050351' has 0 unresolved dependencies Read 11437414 spots for SRR7050351/SRR7050351.sra Written 11437414 spots for SRR7050351/SRR7050351.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:48 34210849 reads; of these: 34210849 (100.00%) were unpaired; of these: 1094075 (3.20%) aligned 0 times 24375010 (71.25%) aligned exactly 1 time 8741764 (25.55%) aligned >1 times 96.80% overall alignment rate Time searching: 00:08:49 Overall time: 00:08:49 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] 4117948 / 33116774 = 0.1243 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 20:44:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981655/SRX3981655.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981655/SRX3981655.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981655/SRX3981655.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981655/SRX3981655.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 20:44:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:44:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:44:45: 1000000 INFO @ Sun, 21 Jun 2020 20:44:50: 2000000 INFO @ Sun, 21 Jun 2020 20:44:55: 3000000 INFO @ Sun, 21 Jun 2020 20:44:59: 4000000 INFO @ Sun, 21 Jun 2020 20:45:04: 5000000 INFO @ Sun, 21 Jun 2020 20:45:08: 6000000 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 20:45:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981655/SRX3981655.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981655/SRX3981655.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981655/SRX3981655.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981655/SRX3981655.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 20:45:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:45:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:45:13: 7000000 INFO @ Sun, 21 Jun 2020 20:45:16: 1000000 INFO @ Sun, 21 Jun 2020 20:45:18: 8000000 INFO @ Sun, 21 Jun 2020 20:45:20: 2000000 INFO @ Sun, 21 Jun 2020 20:45:23: 9000000 INFO @ Sun, 21 Jun 2020 20:45:25: 3000000 INFO @ Sun, 21 Jun 2020 20:45:27: 10000000 INFO @ Sun, 21 Jun 2020 20:45:30: 4000000 INFO @ Sun, 21 Jun 2020 20:45:32: 11000000 INFO @ Sun, 21 Jun 2020 20:45:35: 5000000 INFO @ Sun, 21 Jun 2020 20:45:37: 12000000 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 20:45:39: 6000000 INFO @ Sun, 21 Jun 2020 20:45:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981655/SRX3981655.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981655/SRX3981655.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981655/SRX3981655.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981655/SRX3981655.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 20:45:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:45:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:45:41: 13000000 INFO @ Sun, 21 Jun 2020 20:45:44: 7000000 INFO @ Sun, 21 Jun 2020 20:45:46: 1000000 INFO @ Sun, 21 Jun 2020 20:45:46: 14000000 INFO @ Sun, 21 Jun 2020 20:45:49: 8000000 INFO @ Sun, 21 Jun 2020 20:45:51: 2000000 INFO @ Sun, 21 Jun 2020 20:45:51: 15000000 INFO @ Sun, 21 Jun 2020 20:45:54: 9000000 INFO @ Sun, 21 Jun 2020 20:45:55: 3000000 INFO @ Sun, 21 Jun 2020 20:45:55: 16000000 INFO @ Sun, 21 Jun 2020 20:45:58: 10000000 INFO @ Sun, 21 Jun 2020 20:46:00: 4000000 INFO @ Sun, 21 Jun 2020 20:46:00: 17000000 INFO @ Sun, 21 Jun 2020 20:46:03: 11000000 INFO @ Sun, 21 Jun 2020 20:46:05: 5000000 INFO @ Sun, 21 Jun 2020 20:46:05: 18000000 INFO @ Sun, 21 Jun 2020 20:46:08: 12000000 INFO @ Sun, 21 Jun 2020 20:46:10: 19000000 INFO @ Sun, 21 Jun 2020 20:46:10: 6000000 INFO @ Sun, 21 Jun 2020 20:46:12: 13000000 INFO @ Sun, 21 Jun 2020 20:46:14: 20000000 INFO @ Sun, 21 Jun 2020 20:46:14: 7000000 INFO @ Sun, 21 Jun 2020 20:46:17: 14000000 INFO @ Sun, 21 Jun 2020 20:46:19: 21000000 INFO @ Sun, 21 Jun 2020 20:46:19: 8000000 INFO @ Sun, 21 Jun 2020 20:46:22: 15000000 INFO @ Sun, 21 Jun 2020 20:46:24: 22000000 INFO @ Sun, 21 Jun 2020 20:46:24: 9000000 INFO @ Sun, 21 Jun 2020 20:46:26: 16000000 INFO @ Sun, 21 Jun 2020 20:46:28: 23000000 INFO @ Sun, 21 Jun 2020 20:46:29: 10000000 INFO @ Sun, 21 Jun 2020 20:46:31: 17000000 INFO @ Sun, 21 Jun 2020 20:46:33: 24000000 INFO @ Sun, 21 Jun 2020 20:46:33: 11000000 INFO @ Sun, 21 Jun 2020 20:46:36: 18000000 INFO @ Sun, 21 Jun 2020 20:46:38: 12000000 INFO @ Sun, 21 Jun 2020 20:46:38: 25000000 INFO @ Sun, 21 Jun 2020 20:46:41: 19000000 INFO @ Sun, 21 Jun 2020 20:46:43: 13000000 INFO @ Sun, 21 Jun 2020 20:46:43: 26000000 INFO @ Sun, 21 Jun 2020 20:46:46: 20000000 INFO @ Sun, 21 Jun 2020 20:46:47: 14000000 INFO @ Sun, 21 Jun 2020 20:46:48: 27000000 INFO @ Sun, 21 Jun 2020 20:46:50: 21000000 INFO @ Sun, 21 Jun 2020 20:46:52: 15000000 INFO @ Sun, 21 Jun 2020 20:46:52: 28000000 INFO @ Sun, 21 Jun 2020 20:46:55: 22000000 INFO @ Sun, 21 Jun 2020 20:46:57: 16000000 INFO @ Sun, 21 Jun 2020 20:46:58: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:46:58: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:46:58: #1 total tags in treatment: 28998826 INFO @ Sun, 21 Jun 2020 20:46:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:46:58: #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 20:46:58: #1 tags after filtering in treatment: 28998762 INFO @ Sun, 21 Jun 2020 20:46:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:46:58: #1 finished! INFO @ Sun, 21 Jun 2020 20:46:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:46:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:47:00: 23000000 INFO @ Sun, 21 Jun 2020 20:47:00: #2 number of paired peaks: 266 WARNING @ Sun, 21 Jun 2020 20:47:00: Fewer paired peaks (266) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 266 pairs to build model! INFO @ Sun, 21 Jun 2020 20:47:00: start model_add_line... INFO @ Sun, 21 Jun 2020 20:47:00: start X-correlation... INFO @ Sun, 21 Jun 2020 20:47:00: end of X-cor INFO @ Sun, 21 Jun 2020 20:47:00: #2 finished! INFO @ Sun, 21 Jun 2020 20:47:00: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 20:47:00: #2 alternative fragment length(s) may be 1,46,482,556 bps INFO @ Sun, 21 Jun 2020 20:47:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981655/SRX3981655.05_model.r WARNING @ Sun, 21 Jun 2020 20:47:00: #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 20:47:00: #2 You may need to consider one of the other alternative d(s): 1,46,482,556 WARNING @ Sun, 21 Jun 2020 20:47:00: #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 20:47:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:47:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:47:02: 17000000 INFO @ Sun, 21 Jun 2020 20:47:04: 24000000 INFO @ Sun, 21 Jun 2020 20:47:06: 18000000 INFO @ Sun, 21 Jun 2020 20:47:09: 25000000 INFO @ Sun, 21 Jun 2020 20:47:11: 19000000 INFO @ Sun, 21 Jun 2020 20:47:14: 26000000 INFO @ Sun, 21 Jun 2020 20:47:16: 20000000 INFO @ Sun, 21 Jun 2020 20:47:19: 27000000 INFO @ Sun, 21 Jun 2020 20:47:21: 21000000 INFO @ Sun, 21 Jun 2020 20:47:24: 28000000 INFO @ Sun, 21 Jun 2020 20:47:26: 22000000 INFO @ Sun, 21 Jun 2020 20:47:29: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:47:29: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:47:29: #1 total tags in treatment: 28998826 INFO @ Sun, 21 Jun 2020 20:47:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:47:29: #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 20:47:29: #1 tags after filtering in treatment: 28998762 INFO @ Sun, 21 Jun 2020 20:47:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:47:29: #1 finished! INFO @ Sun, 21 Jun 2020 20:47:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:47:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:47:30: 23000000 INFO @ Sun, 21 Jun 2020 20:47:31: #2 number of paired peaks: 266 WARNING @ Sun, 21 Jun 2020 20:47:31: Fewer paired peaks (266) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 266 pairs to build model! INFO @ Sun, 21 Jun 2020 20:47:31: start model_add_line... INFO @ Sun, 21 Jun 2020 20:47:31: start X-correlation... INFO @ Sun, 21 Jun 2020 20:47:31: end of X-cor INFO @ Sun, 21 Jun 2020 20:47:31: #2 finished! INFO @ Sun, 21 Jun 2020 20:47:31: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 20:47:31: #2 alternative fragment length(s) may be 1,46,482,556 bps INFO @ Sun, 21 Jun 2020 20:47:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981655/SRX3981655.10_model.r WARNING @ Sun, 21 Jun 2020 20:47:31: #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 20:47:31: #2 You may need to consider one of the other alternative d(s): 1,46,482,556 WARNING @ Sun, 21 Jun 2020 20:47:31: #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 20:47:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:47:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:47:35: 24000000 INFO @ Sun, 21 Jun 2020 20:47:40: 25000000 INFO @ Sun, 21 Jun 2020 20:47:44: 26000000 INFO @ Sun, 21 Jun 2020 20:47:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:47:49: 27000000 INFO @ Sun, 21 Jun 2020 20:47:54: 28000000 INFO @ Sun, 21 Jun 2020 20:47:59: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:47:59: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:47:59: #1 total tags in treatment: 28998826 INFO @ Sun, 21 Jun 2020 20:47:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:47:59: #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 20:47:59: #1 tags after filtering in treatment: 28998762 INFO @ Sun, 21 Jun 2020 20:47:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:47:59: #1 finished! INFO @ Sun, 21 Jun 2020 20:47:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:47:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:48:01: #2 number of paired peaks: 266 WARNING @ Sun, 21 Jun 2020 20:48:01: Fewer paired peaks (266) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 266 pairs to build model! INFO @ Sun, 21 Jun 2020 20:48:01: start model_add_line... INFO @ Sun, 21 Jun 2020 20:48:01: start X-correlation... INFO @ Sun, 21 Jun 2020 20:48:01: end of X-cor INFO @ Sun, 21 Jun 2020 20:48:01: #2 finished! INFO @ Sun, 21 Jun 2020 20:48:01: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 20:48:01: #2 alternative fragment length(s) may be 1,46,482,556 bps INFO @ Sun, 21 Jun 2020 20:48:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981655/SRX3981655.20_model.r WARNING @ Sun, 21 Jun 2020 20:48:01: #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 20:48:01: #2 You may need to consider one of the other alternative d(s): 1,46,482,556 WARNING @ Sun, 21 Jun 2020 20:48:01: #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 20:48:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:48:01: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:48:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981655/SRX3981655.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:48:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981655/SRX3981655.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:48:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981655/SRX3981655.05_summits.bed INFO @ Sun, 21 Jun 2020 20:48:07: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:48:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:48:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981655/SRX3981655.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:48:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981655/SRX3981655.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:48:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981655/SRX3981655.10_summits.bed INFO @ Sun, 21 Jun 2020 20:48:38: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:48:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:49:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981655/SRX3981655.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:49:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981655/SRX3981655.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:49:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981655/SRX3981655.20_summits.bed INFO @ Sun, 21 Jun 2020 20:49:07: Done! BigWig に変換しました。 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling