Job ID = 6498739 SRX = SRX749068 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-26T00:01:25 prefetch.2.10.7: 1) Downloading 'SRR1636796'... 2020-06-26T00:01:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:05:16 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:05:16 prefetch.2.10.7: 1) 'SRR1636796' was downloaded successfully Read 20084492 spots for SRR1636796/SRR1636796.sra Written 20084492 spots for SRR1636796/SRR1636796.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: 00:37:16 20084492 reads; of these: 20084492 (100.00%) were paired; of these: 1980993 (9.86%) aligned concordantly 0 times 13152028 (65.48%) aligned concordantly exactly 1 time 4951471 (24.65%) aligned concordantly >1 times ---- 1980993 pairs aligned concordantly 0 times; of these: 12173 (0.61%) aligned discordantly 1 time ---- 1968820 pairs aligned 0 times concordantly or discordantly; of these: 3937640 mates make up the pairs; of these: 3364598 (85.45%) aligned 0 times 403223 (10.24%) aligned exactly 1 time 169819 (4.31%) aligned >1 times 91.62% overall alignment rate Time searching: 00:37:16 Overall time: 00:37:16 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 16 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] 4607893 / 18100885 = 0.2546 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 09:53:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749068/SRX749068.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749068/SRX749068.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749068/SRX749068.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749068/SRX749068.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 09:53:24: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:53:24: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:53:30: 1000000 INFO @ Fri, 26 Jun 2020 09:53:35: 2000000 INFO @ Fri, 26 Jun 2020 09:53:40: 3000000 INFO @ Fri, 26 Jun 2020 09:53:46: 4000000 INFO @ Fri, 26 Jun 2020 09:53:51: 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 @ Fri, 26 Jun 2020 09:53:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749068/SRX749068.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749068/SRX749068.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749068/SRX749068.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749068/SRX749068.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 09:53:55: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:53:55: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:53:56: 6000000 INFO @ Fri, 26 Jun 2020 09:54:01: 1000000 INFO @ Fri, 26 Jun 2020 09:54:02: 7000000 INFO @ Fri, 26 Jun 2020 09:54:07: 2000000 INFO @ Fri, 26 Jun 2020 09:54:08: 8000000 INFO @ Fri, 26 Jun 2020 09:54:13: 3000000 INFO @ Fri, 26 Jun 2020 09:54:14: 9000000 INFO @ Fri, 26 Jun 2020 09:54:19: 4000000 INFO @ Fri, 26 Jun 2020 09:54:20: 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 09:54:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749068/SRX749068.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749068/SRX749068.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749068/SRX749068.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749068/SRX749068.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 09:54:24: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:54:24: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:54:25: 5000000 INFO @ Fri, 26 Jun 2020 09:54:26: 11000000 INFO @ Fri, 26 Jun 2020 09:54:30: 1000000 INFO @ Fri, 26 Jun 2020 09:54:31: 6000000 INFO @ Fri, 26 Jun 2020 09:54:32: 12000000 INFO @ Fri, 26 Jun 2020 09:54:36: 2000000 INFO @ Fri, 26 Jun 2020 09:54:37: 7000000 INFO @ Fri, 26 Jun 2020 09:54:38: 13000000 INFO @ Fri, 26 Jun 2020 09:54:43: 3000000 INFO @ Fri, 26 Jun 2020 09:54:43: 8000000 INFO @ Fri, 26 Jun 2020 09:54:44: 14000000 INFO @ Fri, 26 Jun 2020 09:54:49: 9000000 INFO @ Fri, 26 Jun 2020 09:54:49: 4000000 INFO @ Fri, 26 Jun 2020 09:54:50: 15000000 INFO @ Fri, 26 Jun 2020 09:54:54: 10000000 INFO @ Fri, 26 Jun 2020 09:54:55: 5000000 INFO @ Fri, 26 Jun 2020 09:54:56: 16000000 INFO @ Fri, 26 Jun 2020 09:55:00: 11000000 INFO @ Fri, 26 Jun 2020 09:55:01: 6000000 INFO @ Fri, 26 Jun 2020 09:55:02: 17000000 INFO @ Fri, 26 Jun 2020 09:55:06: 12000000 INFO @ Fri, 26 Jun 2020 09:55:07: 7000000 INFO @ Fri, 26 Jun 2020 09:55:08: 18000000 INFO @ Fri, 26 Jun 2020 09:55:12: 13000000 INFO @ Fri, 26 Jun 2020 09:55:13: 8000000 INFO @ Fri, 26 Jun 2020 09:55:14: 19000000 INFO @ Fri, 26 Jun 2020 09:55:18: 14000000 INFO @ Fri, 26 Jun 2020 09:55:19: 9000000 INFO @ Fri, 26 Jun 2020 09:55:20: 20000000 INFO @ Fri, 26 Jun 2020 09:55:24: 15000000 INFO @ Fri, 26 Jun 2020 09:55:25: 10000000 INFO @ Fri, 26 Jun 2020 09:55:26: 21000000 INFO @ Fri, 26 Jun 2020 09:55:30: 16000000 INFO @ Fri, 26 Jun 2020 09:55:31: 11000000 INFO @ Fri, 26 Jun 2020 09:55:32: 22000000 INFO @ Fri, 26 Jun 2020 09:55:36: 17000000 INFO @ Fri, 26 Jun 2020 09:55:37: 12000000 INFO @ Fri, 26 Jun 2020 09:55:37: 23000000 INFO @ Fri, 26 Jun 2020 09:55:42: 18000000 INFO @ Fri, 26 Jun 2020 09:55:43: 13000000 INFO @ Fri, 26 Jun 2020 09:55:43: 24000000 INFO @ Fri, 26 Jun 2020 09:55:48: 19000000 INFO @ Fri, 26 Jun 2020 09:55:49: 14000000 INFO @ Fri, 26 Jun 2020 09:55:49: 25000000 INFO @ Fri, 26 Jun 2020 09:55:54: 20000000 INFO @ Fri, 26 Jun 2020 09:55:55: 15000000 INFO @ Fri, 26 Jun 2020 09:55:55: 26000000 INFO @ Fri, 26 Jun 2020 09:56:00: 21000000 INFO @ Fri, 26 Jun 2020 09:56:00: 16000000 INFO @ Fri, 26 Jun 2020 09:56:01: 27000000 INFO @ Fri, 26 Jun 2020 09:56:05: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:56:05: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:56:05: #1 total tags in treatment: 13497723 INFO @ Fri, 26 Jun 2020 09:56:05: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:56:05: #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 09:56:05: #1 tags after filtering in treatment: 11936852 INFO @ Fri, 26 Jun 2020 09:56:05: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 26 Jun 2020 09:56:05: #1 finished! INFO @ Fri, 26 Jun 2020 09:56:05: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:56:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:56:05: 22000000 INFO @ Fri, 26 Jun 2020 09:56:06: #2 number of paired peaks: 3067 INFO @ Fri, 26 Jun 2020 09:56:06: start model_add_line... INFO @ Fri, 26 Jun 2020 09:56:06: start X-correlation... INFO @ Fri, 26 Jun 2020 09:56:06: end of X-cor INFO @ Fri, 26 Jun 2020 09:56:06: #2 finished! INFO @ Fri, 26 Jun 2020 09:56:06: #2 predicted fragment length is 148 bps INFO @ Fri, 26 Jun 2020 09:56:06: #2 alternative fragment length(s) may be 148 bps INFO @ Fri, 26 Jun 2020 09:56:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749068/SRX749068.05_model.r INFO @ Fri, 26 Jun 2020 09:56:06: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:56:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:56:06: 17000000 INFO @ Fri, 26 Jun 2020 09:56:11: 23000000 INFO @ Fri, 26 Jun 2020 09:56:12: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:56:17: 24000000 INFO @ Fri, 26 Jun 2020 09:56:18: 19000000 INFO @ Fri, 26 Jun 2020 09:56:23: 25000000 INFO @ Fri, 26 Jun 2020 09:56:24: 20000000 INFO @ Fri, 26 Jun 2020 09:56:29: 26000000 INFO @ Fri, 26 Jun 2020 09:56:30: 21000000 INFO @ Fri, 26 Jun 2020 09:56:34: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:56:35: 27000000 INFO @ Fri, 26 Jun 2020 09:56:36: 22000000 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: 13497723 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 09:56:39: #1 tags after filtering in treatment: 11936852 INFO @ Fri, 26 Jun 2020 09:56:39: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 26 Jun 2020 09:56:39: #1 finished! INFO @ Fri, 26 Jun 2020 09:56:39: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:56:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:56:40: #2 number of paired peaks: 3067 INFO @ Fri, 26 Jun 2020 09:56:40: start model_add_line... INFO @ Fri, 26 Jun 2020 09:56:40: start X-correlation... INFO @ Fri, 26 Jun 2020 09:56:40: end of X-cor INFO @ Fri, 26 Jun 2020 09:56:40: #2 finished! INFO @ Fri, 26 Jun 2020 09:56:40: #2 predicted fragment length is 148 bps INFO @ Fri, 26 Jun 2020 09:56:40: #2 alternative fragment length(s) may be 148 bps INFO @ Fri, 26 Jun 2020 09:56:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749068/SRX749068.10_model.r INFO @ Fri, 26 Jun 2020 09:56:40: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:56:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:56:41: 23000000 INFO @ Fri, 26 Jun 2020 09:56:47: 24000000 INFO @ Fri, 26 Jun 2020 09:56:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749068/SRX749068.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:56:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749068/SRX749068.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:56:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749068/SRX749068.05_summits.bed INFO @ Fri, 26 Jun 2020 09:56:49: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (11617 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:56:52: 25000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 09:56:58: 26000000 INFO @ Fri, 26 Jun 2020 09:57:03: 27000000 INFO @ Fri, 26 Jun 2020 09:57:06: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:57:06: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:57:06: #1 total tags in treatment: 13497723 INFO @ Fri, 26 Jun 2020 09:57:06: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:57:06: #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 09:57:07: #1 tags after filtering in treatment: 11936852 INFO @ Fri, 26 Jun 2020 09:57:07: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 26 Jun 2020 09:57:07: #1 finished! INFO @ Fri, 26 Jun 2020 09:57:07: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:57:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:57:08: #2 number of paired peaks: 3067 INFO @ Fri, 26 Jun 2020 09:57:08: start model_add_line... INFO @ Fri, 26 Jun 2020 09:57:08: start X-correlation... INFO @ Fri, 26 Jun 2020 09:57:08: end of X-cor INFO @ Fri, 26 Jun 2020 09:57:08: #2 finished! INFO @ Fri, 26 Jun 2020 09:57:08: #2 predicted fragment length is 148 bps INFO @ Fri, 26 Jun 2020 09:57:08: #2 alternative fragment length(s) may be 148 bps INFO @ Fri, 26 Jun 2020 09:57:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749068/SRX749068.20_model.r INFO @ Fri, 26 Jun 2020 09:57:08: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:57:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:57:09: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:57:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749068/SRX749068.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:57:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749068/SRX749068.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:57:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749068/SRX749068.10_summits.bed INFO @ Fri, 26 Jun 2020 09:57:23: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (7514 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:57:36: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:57:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749068/SRX749068.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:57:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749068/SRX749068.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:57:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749068/SRX749068.20_summits.bed INFO @ Fri, 26 Jun 2020 09:57:50: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4314 records, 4 fields): 5 millis CompletedMACS2peakCalling