Job ID = 6498736 SRX = SRX749063 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-26T00:28:54 prefetch.2.10.7: 1) Downloading 'SRR1636791'... 2020-06-26T00:28:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:31:54 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:31:54 prefetch.2.10.7: 1) 'SRR1636791' was downloaded successfully Read 16178834 spots for SRR1636791/SRR1636791.sra Written 16178834 spots for SRR1636791/SRR1636791.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: 00:22:28 16178834 reads; of these: 16178834 (100.00%) were paired; of these: 1159038 (7.16%) aligned concordantly 0 times 12414586 (76.73%) aligned concordantly exactly 1 time 2605210 (16.10%) aligned concordantly >1 times ---- 1159038 pairs aligned concordantly 0 times; of these: 127017 (10.96%) aligned discordantly 1 time ---- 1032021 pairs aligned 0 times concordantly or discordantly; of these: 2064042 mates make up the pairs; of these: 1418220 (68.71%) aligned 0 times 465724 (22.56%) aligned exactly 1 time 180098 (8.73%) aligned >1 times 95.62% overall alignment rate Time searching: 00:22:28 Overall time: 00:22:28 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] 730913 / 15129239 = 0.0483 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 10:05:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749063/SRX749063.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749063/SRX749063.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749063/SRX749063.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749063/SRX749063.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 10:05:16: #1 read tag files... INFO @ Fri, 26 Jun 2020 10:05:16: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 10:05:22: 1000000 INFO @ Fri, 26 Jun 2020 10:05:28: 2000000 INFO @ Fri, 26 Jun 2020 10:05:34: 3000000 INFO @ Fri, 26 Jun 2020 10:05:40: 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 10:05:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749063/SRX749063.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749063/SRX749063.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749063/SRX749063.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749063/SRX749063.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 10:05:45: #1 read tag files... INFO @ Fri, 26 Jun 2020 10:05:45: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 10:05:46: 5000000 INFO @ Fri, 26 Jun 2020 10:05:52: 1000000 INFO @ Fri, 26 Jun 2020 10:05:52: 6000000 INFO @ Fri, 26 Jun 2020 10:05:58: 2000000 INFO @ Fri, 26 Jun 2020 10:05:59: 7000000 INFO @ Fri, 26 Jun 2020 10:06:05: 3000000 INFO @ Fri, 26 Jun 2020 10:06:05: 8000000 INFO @ Fri, 26 Jun 2020 10:06:11: 9000000 INFO @ Fri, 26 Jun 2020 10:06:11: 4000000 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 10:06:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX749063/SRX749063.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX749063/SRX749063.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX749063/SRX749063.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX749063/SRX749063.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 10:06:15: #1 read tag files... INFO @ Fri, 26 Jun 2020 10:06:15: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 10:06:18: 10000000 INFO @ Fri, 26 Jun 2020 10:06:18: 5000000 INFO @ Fri, 26 Jun 2020 10:06:22: 1000000 INFO @ Fri, 26 Jun 2020 10:06:24: 11000000 INFO @ Fri, 26 Jun 2020 10:06:24: 6000000 INFO @ Fri, 26 Jun 2020 10:06:28: 2000000 INFO @ Fri, 26 Jun 2020 10:06:30: 12000000 INFO @ Fri, 26 Jun 2020 10:06:31: 7000000 INFO @ Fri, 26 Jun 2020 10:06:34: 3000000 INFO @ Fri, 26 Jun 2020 10:06:37: 13000000 INFO @ Fri, 26 Jun 2020 10:06:37: 8000000 INFO @ Fri, 26 Jun 2020 10:06:41: 4000000 INFO @ Fri, 26 Jun 2020 10:06:43: 14000000 INFO @ Fri, 26 Jun 2020 10:06:44: 9000000 INFO @ Fri, 26 Jun 2020 10:06:47: 5000000 INFO @ Fri, 26 Jun 2020 10:06:49: 15000000 INFO @ Fri, 26 Jun 2020 10:06:50: 10000000 INFO @ Fri, 26 Jun 2020 10:06:54: 6000000 INFO @ Fri, 26 Jun 2020 10:06:56: 16000000 INFO @ Fri, 26 Jun 2020 10:06:57: 11000000 INFO @ Fri, 26 Jun 2020 10:07:00: 7000000 INFO @ Fri, 26 Jun 2020 10:07:02: 17000000 INFO @ Fri, 26 Jun 2020 10:07:03: 12000000 INFO @ Fri, 26 Jun 2020 10:07:06: 8000000 INFO @ Fri, 26 Jun 2020 10:07:08: 18000000 INFO @ Fri, 26 Jun 2020 10:07:10: 13000000 INFO @ Fri, 26 Jun 2020 10:07:13: 9000000 INFO @ Fri, 26 Jun 2020 10:07:15: 19000000 INFO @ Fri, 26 Jun 2020 10:07:17: 14000000 INFO @ Fri, 26 Jun 2020 10:07:19: 10000000 INFO @ Fri, 26 Jun 2020 10:07:21: 20000000 INFO @ Fri, 26 Jun 2020 10:07:23: 15000000 INFO @ Fri, 26 Jun 2020 10:07:25: 11000000 INFO @ Fri, 26 Jun 2020 10:07:27: 21000000 INFO @ Fri, 26 Jun 2020 10:07:29: 16000000 INFO @ Fri, 26 Jun 2020 10:07:31: 12000000 INFO @ Fri, 26 Jun 2020 10:07:34: 22000000 INFO @ Fri, 26 Jun 2020 10:07:36: 17000000 INFO @ Fri, 26 Jun 2020 10:07:38: 13000000 INFO @ Fri, 26 Jun 2020 10:07:40: 23000000 INFO @ Fri, 26 Jun 2020 10:07:42: 18000000 INFO @ Fri, 26 Jun 2020 10:07:44: 14000000 INFO @ Fri, 26 Jun 2020 10:07:47: 24000000 INFO @ Fri, 26 Jun 2020 10:07:49: 19000000 INFO @ Fri, 26 Jun 2020 10:07:50: 15000000 INFO @ Fri, 26 Jun 2020 10:07:53: 25000000 INFO @ Fri, 26 Jun 2020 10:07:55: 20000000 INFO @ Fri, 26 Jun 2020 10:07:57: 16000000 INFO @ Fri, 26 Jun 2020 10:07:59: 26000000 INFO @ Fri, 26 Jun 2020 10:08:02: 21000000 INFO @ Fri, 26 Jun 2020 10:08:03: 17000000 INFO @ Fri, 26 Jun 2020 10:08:06: 27000000 INFO @ Fri, 26 Jun 2020 10:08:08: 22000000 INFO @ Fri, 26 Jun 2020 10:08:09: 18000000 INFO @ Fri, 26 Jun 2020 10:08:12: 28000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 10:08:15: 23000000 INFO @ Fri, 26 Jun 2020 10:08:16: 19000000 INFO @ Fri, 26 Jun 2020 10:08:19: 29000000 INFO @ Fri, 26 Jun 2020 10:08:21: 24000000 INFO @ Fri, 26 Jun 2020 10:08:22: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 10:08:22: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 10:08:22: #1 total tags in treatment: 14290453 INFO @ Fri, 26 Jun 2020 10:08:22: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 10:08:22: #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 10:08:22: 20000000 INFO @ Fri, 26 Jun 2020 10:08:22: #1 tags after filtering in treatment: 10749326 INFO @ Fri, 26 Jun 2020 10:08:22: #1 Redundant rate of treatment: 0.25 INFO @ Fri, 26 Jun 2020 10:08:22: #1 finished! INFO @ Fri, 26 Jun 2020 10:08:22: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 10:08:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 10:08:23: #2 number of paired peaks: 6124 INFO @ Fri, 26 Jun 2020 10:08:23: start model_add_line... INFO @ Fri, 26 Jun 2020 10:08:23: start X-correlation... INFO @ Fri, 26 Jun 2020 10:08:24: end of X-cor INFO @ Fri, 26 Jun 2020 10:08:24: #2 finished! INFO @ Fri, 26 Jun 2020 10:08:24: #2 predicted fragment length is 171 bps INFO @ Fri, 26 Jun 2020 10:08:24: #2 alternative fragment length(s) may be 171 bps INFO @ Fri, 26 Jun 2020 10:08:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749063/SRX749063.05_model.r INFO @ Fri, 26 Jun 2020 10:08:24: #3 Call peaks... INFO @ Fri, 26 Jun 2020 10:08:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 10:08:28: 25000000 INFO @ Fri, 26 Jun 2020 10:08:28: 21000000 INFO @ Fri, 26 Jun 2020 10:08:35: 26000000 INFO @ Fri, 26 Jun 2020 10:08:35: 22000000 INFO @ Fri, 26 Jun 2020 10:08:41: 27000000 INFO @ Fri, 26 Jun 2020 10:08:41: 23000000 INFO @ Fri, 26 Jun 2020 10:08:48: 24000000 INFO @ Fri, 26 Jun 2020 10:08:48: 28000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 10:08:54: 25000000 INFO @ Fri, 26 Jun 2020 10:08:54: 29000000 INFO @ Fri, 26 Jun 2020 10:08:58: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 10:08:58: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 10:08:58: #1 total tags in treatment: 14290453 INFO @ Fri, 26 Jun 2020 10:08:58: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 10:08:58: #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 10:08:58: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 10:08:58: #1 tags after filtering in treatment: 10749326 INFO @ Fri, 26 Jun 2020 10:08:58: #1 Redundant rate of treatment: 0.25 INFO @ Fri, 26 Jun 2020 10:08:58: #1 finished! INFO @ Fri, 26 Jun 2020 10:08:58: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 10:08:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 10:08:59: #2 number of paired peaks: 6124 INFO @ Fri, 26 Jun 2020 10:08:59: start model_add_line... INFO @ Fri, 26 Jun 2020 10:08:59: start X-correlation... INFO @ Fri, 26 Jun 2020 10:08:59: end of X-cor INFO @ Fri, 26 Jun 2020 10:08:59: #2 finished! INFO @ Fri, 26 Jun 2020 10:08:59: #2 predicted fragment length is 171 bps INFO @ Fri, 26 Jun 2020 10:08:59: #2 alternative fragment length(s) may be 171 bps INFO @ Fri, 26 Jun 2020 10:08:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749063/SRX749063.10_model.r INFO @ Fri, 26 Jun 2020 10:08:59: #3 Call peaks... INFO @ Fri, 26 Jun 2020 10:08:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 10:09:01: 26000000 INFO @ Fri, 26 Jun 2020 10:09:07: 27000000 INFO @ Fri, 26 Jun 2020 10:09:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749063/SRX749063.05_peaks.xls INFO @ Fri, 26 Jun 2020 10:09:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749063/SRX749063.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 10:09:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749063/SRX749063.05_summits.bed INFO @ Fri, 26 Jun 2020 10:09:12: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (11008 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 10:09:13: 28000000 INFO @ Fri, 26 Jun 2020 10:09:19: 29000000 INFO @ Fri, 26 Jun 2020 10:09:22: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 10:09:22: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 10:09:22: #1 total tags in treatment: 14290453 INFO @ Fri, 26 Jun 2020 10:09:22: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 10:09:22: #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 10:09:23: #1 tags after filtering in treatment: 10749326 INFO @ Fri, 26 Jun 2020 10:09:23: #1 Redundant rate of treatment: 0.25 INFO @ Fri, 26 Jun 2020 10:09:23: #1 finished! INFO @ Fri, 26 Jun 2020 10:09:23: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 10:09:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 10:09:24: #2 number of paired peaks: 6124 INFO @ Fri, 26 Jun 2020 10:09:24: start model_add_line... INFO @ Fri, 26 Jun 2020 10:09:24: start X-correlation... INFO @ Fri, 26 Jun 2020 10:09:24: end of X-cor INFO @ Fri, 26 Jun 2020 10:09:24: #2 finished! INFO @ Fri, 26 Jun 2020 10:09:24: #2 predicted fragment length is 171 bps INFO @ Fri, 26 Jun 2020 10:09:24: #2 alternative fragment length(s) may be 171 bps INFO @ Fri, 26 Jun 2020 10:09:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX749063/SRX749063.20_model.r INFO @ Fri, 26 Jun 2020 10:09:24: #3 Call peaks... INFO @ Fri, 26 Jun 2020 10:09:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 10:09:34: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 10:09:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749063/SRX749063.10_peaks.xls INFO @ Fri, 26 Jun 2020 10:09:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749063/SRX749063.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 10:09:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749063/SRX749063.10_summits.bed INFO @ Fri, 26 Jun 2020 10:09:49: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8962 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 10:09:58: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 10:10:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX749063/SRX749063.20_peaks.xls INFO @ Fri, 26 Jun 2020 10:10:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX749063/SRX749063.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 10:10:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX749063/SRX749063.20_summits.bed INFO @ Fri, 26 Jun 2020 10:10:12: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6583 records, 4 fields): 9 millis CompletedMACS2peakCalling