Job ID = 6498723 SRX = SRX749042 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-26T00:00:25 prefetch.2.10.7: 1) Downloading 'SRR1636770'... 2020-06-26T00:00:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:05:15 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:05:15 prefetch.2.10.7: 1) 'SRR1636770' was downloaded successfully Read 24130276 spots for SRR1636770/SRR1636770.sra Written 24130276 spots for SRR1636770/SRR1636770.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: 00:32:37 24130276 reads; of these: 24130276 (100.00%) were paired; of these: 2539767 (10.53%) aligned concordantly 0 times 17716704 (73.42%) aligned concordantly exactly 1 time 3873805 (16.05%) aligned concordantly >1 times ---- 2539767 pairs aligned concordantly 0 times; of these: 9620 (0.38%) aligned discordantly 1 time ---- 2530147 pairs aligned 0 times concordantly or discordantly; of these: 5060294 mates make up the pairs; of these: 4599226 (90.89%) aligned 0 times 375666 (7.42%) aligned exactly 1 time 85402 (1.69%) aligned >1 times 90.47% overall alignment rate Time searching: 00:32:37 Overall time: 00:32:37 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 20 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 2358494 / 21590292 = 0.1092 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 @ Fri, 26 Jun 2020 09:51:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749042/SRX749042.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749042/SRX749042.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749042/SRX749042.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749042/SRX749042.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 @ Fri, 26 Jun 2020 09:51:56: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:51:56: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:52:01: 1000000 INFO @ Fri, 26 Jun 2020 09:52:06: 2000000 INFO @ Fri, 26 Jun 2020 09:52:12: 3000000 INFO @ Fri, 26 Jun 2020 09:52:18: 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 @ Fri, 26 Jun 2020 09:52:23: 5000000 INFO @ Fri, 26 Jun 2020 09:52:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749042/SRX749042.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749042/SRX749042.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749042/SRX749042.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749042/SRX749042.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 @ Fri, 26 Jun 2020 09:52:24: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:52:24: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:52:29: 6000000 INFO @ Fri, 26 Jun 2020 09:52:30: 1000000 INFO @ Fri, 26 Jun 2020 09:52:34: 7000000 INFO @ Fri, 26 Jun 2020 09:52:36: 2000000 INFO @ Fri, 26 Jun 2020 09:52:40: 8000000 INFO @ Fri, 26 Jun 2020 09:52:42: 3000000 INFO @ Fri, 26 Jun 2020 09:52:46: 9000000 INFO @ Fri, 26 Jun 2020 09:52:47: 4000000 INFO @ Fri, 26 Jun 2020 09:52:51: 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 @ Fri, 26 Jun 2020 09:52:53: 5000000 INFO @ Fri, 26 Jun 2020 09:52:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749042/SRX749042.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749042/SRX749042.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749042/SRX749042.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749042/SRX749042.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 @ Fri, 26 Jun 2020 09:52:54: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:52:54: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:52:57: 11000000 INFO @ Fri, 26 Jun 2020 09:52:59: 6000000 INFO @ Fri, 26 Jun 2020 09:53:00: 1000000 INFO @ Fri, 26 Jun 2020 09:53:03: 12000000 INFO @ Fri, 26 Jun 2020 09:53:05: 7000000 INFO @ Fri, 26 Jun 2020 09:53:06: 2000000 INFO @ Fri, 26 Jun 2020 09:53:09: 13000000 INFO @ Fri, 26 Jun 2020 09:53:10: 8000000 INFO @ Fri, 26 Jun 2020 09:53:12: 3000000 INFO @ Fri, 26 Jun 2020 09:53:15: 14000000 INFO @ Fri, 26 Jun 2020 09:53:16: 9000000 INFO @ Fri, 26 Jun 2020 09:53:18: 4000000 INFO @ Fri, 26 Jun 2020 09:53:20: 15000000 INFO @ Fri, 26 Jun 2020 09:53:22: 10000000 INFO @ Fri, 26 Jun 2020 09:53:23: 5000000 INFO @ Fri, 26 Jun 2020 09:53:26: 16000000 INFO @ Fri, 26 Jun 2020 09:53:28: 11000000 INFO @ Fri, 26 Jun 2020 09:53:29: 6000000 INFO @ Fri, 26 Jun 2020 09:53:32: 17000000 INFO @ Fri, 26 Jun 2020 09:53:33: 12000000 INFO @ Fri, 26 Jun 2020 09:53:35: 7000000 INFO @ Fri, 26 Jun 2020 09:53:38: 18000000 INFO @ Fri, 26 Jun 2020 09:53:39: 13000000 INFO @ Fri, 26 Jun 2020 09:53:41: 8000000 INFO @ Fri, 26 Jun 2020 09:53:43: 19000000 INFO @ Fri, 26 Jun 2020 09:53:45: 14000000 INFO @ Fri, 26 Jun 2020 09:53:46: 9000000 INFO @ Fri, 26 Jun 2020 09:53:49: 20000000 INFO @ Fri, 26 Jun 2020 09:53:51: 15000000 INFO @ Fri, 26 Jun 2020 09:53:52: 10000000 INFO @ Fri, 26 Jun 2020 09:53:55: 21000000 INFO @ Fri, 26 Jun 2020 09:53:57: 16000000 INFO @ Fri, 26 Jun 2020 09:53:58: 11000000 INFO @ Fri, 26 Jun 2020 09:54:01: 22000000 INFO @ Fri, 26 Jun 2020 09:54:02: 17000000 INFO @ Fri, 26 Jun 2020 09:54:04: 12000000 INFO @ Fri, 26 Jun 2020 09:54:06: 23000000 INFO @ Fri, 26 Jun 2020 09:54:08: 18000000 INFO @ Fri, 26 Jun 2020 09:54:09: 13000000 INFO @ Fri, 26 Jun 2020 09:54:12: 24000000 INFO @ Fri, 26 Jun 2020 09:54:14: 19000000 INFO @ Fri, 26 Jun 2020 09:54:15: 14000000 INFO @ Fri, 26 Jun 2020 09:54:18: 25000000 INFO @ Fri, 26 Jun 2020 09:54:20: 20000000 INFO @ Fri, 26 Jun 2020 09:54:21: 15000000 INFO @ Fri, 26 Jun 2020 09:54:24: 26000000 INFO @ Fri, 26 Jun 2020 09:54:26: 21000000 INFO @ Fri, 26 Jun 2020 09:54:27: 16000000 INFO @ Fri, 26 Jun 2020 09:54:29: 27000000 INFO @ Fri, 26 Jun 2020 09:54:31: 22000000 INFO @ Fri, 26 Jun 2020 09:54:33: 17000000 INFO @ Fri, 26 Jun 2020 09:54:35: 28000000 INFO @ Fri, 26 Jun 2020 09:54:37: 23000000 INFO @ Fri, 26 Jun 2020 09:54:38: 18000000 INFO @ Fri, 26 Jun 2020 09:54:41: 29000000 INFO @ Fri, 26 Jun 2020 09:54:43: 24000000 INFO @ Fri, 26 Jun 2020 09:54:44: 19000000 INFO @ Fri, 26 Jun 2020 09:54:47: 30000000 INFO @ Fri, 26 Jun 2020 09:54:49: 25000000 INFO @ Fri, 26 Jun 2020 09:54:50: 20000000 INFO @ Fri, 26 Jun 2020 09:54:53: 31000000 INFO @ Fri, 26 Jun 2020 09:54:54: 26000000 INFO @ Fri, 26 Jun 2020 09:54:56: 21000000 INFO @ Fri, 26 Jun 2020 09:54:59: 32000000 INFO @ Fri, 26 Jun 2020 09:55:00: 27000000 INFO @ Fri, 26 Jun 2020 09:55:01: 22000000 INFO @ Fri, 26 Jun 2020 09:55:04: 33000000 INFO @ Fri, 26 Jun 2020 09:55:06: 28000000 INFO @ Fri, 26 Jun 2020 09:55:07: 23000000 INFO @ Fri, 26 Jun 2020 09:55:10: 34000000 INFO @ Fri, 26 Jun 2020 09:55:12: 29000000 INFO @ Fri, 26 Jun 2020 09:55:13: 24000000 INFO @ Fri, 26 Jun 2020 09:55:16: 35000000 INFO @ Fri, 26 Jun 2020 09:55:18: 30000000 INFO @ Fri, 26 Jun 2020 09:55:19: 25000000 INFO @ Fri, 26 Jun 2020 09:55:21: 36000000 INFO @ Fri, 26 Jun 2020 09:55:23: 31000000 INFO @ Fri, 26 Jun 2020 09:55:24: 26000000 INFO @ Fri, 26 Jun 2020 09:55:27: 37000000 INFO @ Fri, 26 Jun 2020 09:55:29: 32000000 INFO @ Fri, 26 Jun 2020 09:55:30: 27000000 INFO @ Fri, 26 Jun 2020 09:55:33: 38000000 INFO @ Fri, 26 Jun 2020 09:55:35: 33000000 INFO @ Fri, 26 Jun 2020 09:55:36: 28000000 INFO @ Fri, 26 Jun 2020 09:55:39: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:55:39: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:55:39: #1 total tags in treatment: 19232355 INFO @ Fri, 26 Jun 2020 09:55:39: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:55:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:55:39: #1 tags after filtering in treatment: 15408151 INFO @ Fri, 26 Jun 2020 09:55:39: #1 Redundant rate of treatment: 0.20 INFO @ Fri, 26 Jun 2020 09:55:39: #1 finished! INFO @ Fri, 26 Jun 2020 09:55:39: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:55:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:55:40: #2 number of paired peaks: 1118 INFO @ Fri, 26 Jun 2020 09:55:40: start model_add_line... INFO @ Fri, 26 Jun 2020 09:55:40: start X-correlation... INFO @ Fri, 26 Jun 2020 09:55:40: end of X-cor INFO @ Fri, 26 Jun 2020 09:55:40: #2 finished! INFO @ Fri, 26 Jun 2020 09:55:40: #2 predicted fragment length is 116 bps INFO @ Fri, 26 Jun 2020 09:55:40: #2 alternative fragment length(s) may be 116 bps INFO @ Fri, 26 Jun 2020 09:55:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749042/SRX749042.05_model.r INFO @ Fri, 26 Jun 2020 09:55:40: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:55:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:55:41: 34000000 INFO @ Fri, 26 Jun 2020 09:55:42: 29000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:55:46: 35000000 INFO @ Fri, 26 Jun 2020 09:55:48: 30000000 INFO @ Fri, 26 Jun 2020 09:55:52: 36000000 INFO @ Fri, 26 Jun 2020 09:55:53: 31000000 INFO @ Fri, 26 Jun 2020 09:55:58: 37000000 INFO @ Fri, 26 Jun 2020 09:55:59: 32000000 INFO @ Fri, 26 Jun 2020 09:56:03: 38000000 INFO @ Fri, 26 Jun 2020 09:56:05: 33000000 INFO @ Fri, 26 Jun 2020 09:56:09: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:56:09: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:56:09: #1 total tags in treatment: 19232355 INFO @ Fri, 26 Jun 2020 09:56:09: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:56:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:56:09: #1 tags after filtering in treatment: 15408151 INFO @ Fri, 26 Jun 2020 09:56:09: #1 Redundant rate of treatment: 0.20 INFO @ Fri, 26 Jun 2020 09:56:09: #1 finished! INFO @ Fri, 26 Jun 2020 09:56:09: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:56:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:56:10: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:56:10: #2 number of paired peaks: 1118 INFO @ Fri, 26 Jun 2020 09:56:10: start model_add_line... INFO @ Fri, 26 Jun 2020 09:56:11: 34000000 INFO @ Fri, 26 Jun 2020 09:56:11: start X-correlation... INFO @ Fri, 26 Jun 2020 09:56:11: end of X-cor INFO @ Fri, 26 Jun 2020 09:56:11: #2 finished! INFO @ Fri, 26 Jun 2020 09:56:11: #2 predicted fragment length is 116 bps INFO @ Fri, 26 Jun 2020 09:56:11: #2 alternative fragment length(s) may be 116 bps INFO @ Fri, 26 Jun 2020 09:56:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749042/SRX749042.10_model.r INFO @ Fri, 26 Jun 2020 09:56:11: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:56:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:56:16: 35000000 INFO @ Fri, 26 Jun 2020 09:56:21: 36000000 INFO @ Fri, 26 Jun 2020 09:56:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749042/SRX749042.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:56:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749042/SRX749042.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:56:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749042/SRX749042.05_summits.bed INFO @ Fri, 26 Jun 2020 09:56:26: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (11776 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:56:27: 37000000 INFO @ Fri, 26 Jun 2020 09:56:32: 38000000 INFO @ Fri, 26 Jun 2020 09:56:38: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:56:38: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:56:38: #1 total tags in treatment: 19232355 INFO @ Fri, 26 Jun 2020 09:56:38: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:56:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:56:38: #1 tags after filtering in treatment: 15408151 INFO @ Fri, 26 Jun 2020 09:56:38: #1 Redundant rate of treatment: 0.20 INFO @ Fri, 26 Jun 2020 09:56:38: #1 finished! INFO @ Fri, 26 Jun 2020 09:56:38: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:56:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:56:39: #2 number of paired peaks: 1118 INFO @ Fri, 26 Jun 2020 09:56:39: start model_add_line... INFO @ Fri, 26 Jun 2020 09:56:39: start X-correlation... INFO @ Fri, 26 Jun 2020 09:56:39: end of X-cor INFO @ Fri, 26 Jun 2020 09:56:39: #2 finished! INFO @ Fri, 26 Jun 2020 09:56:39: #2 predicted fragment length is 116 bps INFO @ Fri, 26 Jun 2020 09:56:39: #2 alternative fragment length(s) may be 116 bps INFO @ Fri, 26 Jun 2020 09:56:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749042/SRX749042.20_model.r INFO @ Fri, 26 Jun 2020 09:56:39: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:56:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:56:40: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 09:56:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749042/SRX749042.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:56:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749042/SRX749042.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:56:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749042/SRX749042.10_summits.bed INFO @ Fri, 26 Jun 2020 09:56:56: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7194 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:57:11: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:57:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749042/SRX749042.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:57:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749042/SRX749042.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:57:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749042/SRX749042.20_summits.bed INFO @ Fri, 26 Jun 2020 09:57:28: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4686 records, 4 fields): 6 millis CompletedMACS2peakCalling