Job ID = 6497692 SRX = SRX1021226 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T22:41:57 prefetch.2.10.7: 1) Downloading 'SRR2013423'... 2020-06-25T22:41:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:45:35 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:45:35 prefetch.2.10.7: 1) 'SRR2013423' was downloaded successfully Read 14661296 spots for SRR2013423/SRR2013423.sra Written 14661296 spots for SRR2013423/SRR2013423.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: 00:37:50 14661296 reads; of these: 14661296 (100.00%) were paired; of these: 1000486 (6.82%) aligned concordantly 0 times 8749348 (59.68%) aligned concordantly exactly 1 time 4911462 (33.50%) aligned concordantly >1 times ---- 1000486 pairs aligned concordantly 0 times; of these: 21714 (2.17%) aligned discordantly 1 time ---- 978772 pairs aligned 0 times concordantly or discordantly; of these: 1957544 mates make up the pairs; of these: 1527607 (78.04%) aligned 0 times 285382 (14.58%) aligned exactly 1 time 144555 (7.38%) aligned >1 times 94.79% overall alignment rate Time searching: 00:37:50 Overall time: 00:37:50 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 12 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] 2132092 / 13663786 = 0.1560 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 08:34:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1021226/SRX1021226.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1021226/SRX1021226.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1021226/SRX1021226.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1021226/SRX1021226.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 08:34:46: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:34:46: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:34:55: 1000000 INFO @ Fri, 26 Jun 2020 08:35:03: 2000000 INFO @ Fri, 26 Jun 2020 08:35:11: 3000000 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 08:35:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1021226/SRX1021226.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1021226/SRX1021226.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1021226/SRX1021226.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1021226/SRX1021226.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 08:35:16: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:35:16: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:35:20: 4000000 INFO @ Fri, 26 Jun 2020 08:35:24: 1000000 INFO @ Fri, 26 Jun 2020 08:35:29: 5000000 INFO @ Fri, 26 Jun 2020 08:35:33: 2000000 INFO @ Fri, 26 Jun 2020 08:35:38: 6000000 INFO @ Fri, 26 Jun 2020 08:35:41: 3000000 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 08:35:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1021226/SRX1021226.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1021226/SRX1021226.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1021226/SRX1021226.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1021226/SRX1021226.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 08:35:46: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:35:46: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:35:47: 7000000 INFO @ Fri, 26 Jun 2020 08:35:49: 4000000 INFO @ Fri, 26 Jun 2020 08:35:55: 1000000 INFO @ Fri, 26 Jun 2020 08:35:57: 8000000 INFO @ Fri, 26 Jun 2020 08:35:58: 5000000 INFO @ Fri, 26 Jun 2020 08:36:03: 2000000 INFO @ Fri, 26 Jun 2020 08:36:06: 6000000 INFO @ Fri, 26 Jun 2020 08:36:07: 9000000 INFO @ Fri, 26 Jun 2020 08:36:12: 3000000 INFO @ Fri, 26 Jun 2020 08:36:15: 7000000 INFO @ Fri, 26 Jun 2020 08:36:17: 10000000 INFO @ Fri, 26 Jun 2020 08:36:20: 4000000 INFO @ Fri, 26 Jun 2020 08:36:23: 8000000 INFO @ Fri, 26 Jun 2020 08:36:27: 11000000 INFO @ Fri, 26 Jun 2020 08:36:29: 5000000 INFO @ Fri, 26 Jun 2020 08:36:32: 9000000 INFO @ Fri, 26 Jun 2020 08:36:37: 12000000 INFO @ Fri, 26 Jun 2020 08:36:37: 6000000 INFO @ Fri, 26 Jun 2020 08:36:40: 10000000 INFO @ Fri, 26 Jun 2020 08:36:46: 7000000 INFO @ Fri, 26 Jun 2020 08:36:47: 13000000 INFO @ Fri, 26 Jun 2020 08:36:49: 11000000 INFO @ Fri, 26 Jun 2020 08:36:54: 8000000 INFO @ Fri, 26 Jun 2020 08:36:56: 14000000 INFO @ Fri, 26 Jun 2020 08:36:57: 12000000 INFO @ Fri, 26 Jun 2020 08:37:02: 9000000 INFO @ Fri, 26 Jun 2020 08:37:06: 13000000 INFO @ Fri, 26 Jun 2020 08:37:06: 15000000 INFO @ Fri, 26 Jun 2020 08:37:11: 10000000 INFO @ Fri, 26 Jun 2020 08:37:14: 14000000 INFO @ Fri, 26 Jun 2020 08:37:15: 16000000 INFO @ Fri, 26 Jun 2020 08:37:19: 11000000 INFO @ Fri, 26 Jun 2020 08:37:22: 15000000 INFO @ Fri, 26 Jun 2020 08:37:25: 17000000 INFO @ Fri, 26 Jun 2020 08:37:27: 12000000 INFO @ Fri, 26 Jun 2020 08:37:31: 16000000 INFO @ Fri, 26 Jun 2020 08:37:34: 18000000 INFO @ Fri, 26 Jun 2020 08:37:36: 13000000 INFO @ Fri, 26 Jun 2020 08:37:39: 17000000 INFO @ Fri, 26 Jun 2020 08:37:44: 14000000 INFO @ Fri, 26 Jun 2020 08:37:44: 19000000 INFO @ Fri, 26 Jun 2020 08:37:48: 18000000 INFO @ Fri, 26 Jun 2020 08:37:52: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:37:54: 20000000 INFO @ Fri, 26 Jun 2020 08:37:56: 19000000 INFO @ Fri, 26 Jun 2020 08:38:01: 16000000 INFO @ Fri, 26 Jun 2020 08:38:03: 21000000 INFO @ Fri, 26 Jun 2020 08:38:04: 20000000 INFO @ Fri, 26 Jun 2020 08:38:09: 17000000 INFO @ Fri, 26 Jun 2020 08:38:12: 21000000 INFO @ Fri, 26 Jun 2020 08:38:13: 22000000 INFO @ Fri, 26 Jun 2020 08:38:17: 18000000 INFO @ Fri, 26 Jun 2020 08:38:21: 22000000 INFO @ Fri, 26 Jun 2020 08:38:23: 23000000 INFO @ Fri, 26 Jun 2020 08:38:25: 19000000 INFO @ Fri, 26 Jun 2020 08:38:28: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:38:28: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:38:28: #1 total tags in treatment: 11529932 INFO @ Fri, 26 Jun 2020 08:38:28: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:38:28: #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 08:38:28: #1 tags after filtering in treatment: 10715848 INFO @ Fri, 26 Jun 2020 08:38:28: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 26 Jun 2020 08:38:28: #1 finished! INFO @ Fri, 26 Jun 2020 08:38:28: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:38:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:38:29: 23000000 INFO @ Fri, 26 Jun 2020 08:38:29: #2 number of paired peaks: 693 WARNING @ Fri, 26 Jun 2020 08:38:29: Fewer paired peaks (693) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 693 pairs to build model! INFO @ Fri, 26 Jun 2020 08:38:29: start model_add_line... INFO @ Fri, 26 Jun 2020 08:38:29: start X-correlation... INFO @ Fri, 26 Jun 2020 08:38:29: end of X-cor INFO @ Fri, 26 Jun 2020 08:38:29: #2 finished! INFO @ Fri, 26 Jun 2020 08:38:29: #2 predicted fragment length is 114 bps INFO @ Fri, 26 Jun 2020 08:38:29: #2 alternative fragment length(s) may be 114 bps INFO @ Fri, 26 Jun 2020 08:38:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1021226/SRX1021226.05_model.r INFO @ Fri, 26 Jun 2020 08:38:29: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:38:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:38:33: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:38:33: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:38:33: #1 total tags in treatment: 11529932 INFO @ Fri, 26 Jun 2020 08:38:33: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:38:33: #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 08:38:33: #1 tags after filtering in treatment: 10715848 INFO @ Fri, 26 Jun 2020 08:38:33: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 26 Jun 2020 08:38:33: #1 finished! INFO @ Fri, 26 Jun 2020 08:38:33: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:38:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:38:33: 20000000 INFO @ Fri, 26 Jun 2020 08:38:34: #2 number of paired peaks: 693 WARNING @ Fri, 26 Jun 2020 08:38:34: Fewer paired peaks (693) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 693 pairs to build model! INFO @ Fri, 26 Jun 2020 08:38:34: start model_add_line... INFO @ Fri, 26 Jun 2020 08:38:34: start X-correlation... INFO @ Fri, 26 Jun 2020 08:38:34: end of X-cor INFO @ Fri, 26 Jun 2020 08:38:34: #2 finished! INFO @ Fri, 26 Jun 2020 08:38:34: #2 predicted fragment length is 114 bps INFO @ Fri, 26 Jun 2020 08:38:34: #2 alternative fragment length(s) may be 114 bps INFO @ Fri, 26 Jun 2020 08:38:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1021226/SRX1021226.10_model.r INFO @ Fri, 26 Jun 2020 08:38:34: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:38:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:38:40: 21000000 INFO @ Fri, 26 Jun 2020 08:38:46: 22000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 08:38:53: 23000000 INFO @ Fri, 26 Jun 2020 08:38:55: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:38:57: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:38:57: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:38:57: #1 total tags in treatment: 11529932 INFO @ Fri, 26 Jun 2020 08:38:57: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:38:57: #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 08:38:57: #1 tags after filtering in treatment: 10715848 INFO @ Fri, 26 Jun 2020 08:38:57: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 26 Jun 2020 08:38:57: #1 finished! INFO @ Fri, 26 Jun 2020 08:38:57: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:38:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:38:58: #2 number of paired peaks: 693 WARNING @ Fri, 26 Jun 2020 08:38:58: Fewer paired peaks (693) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 693 pairs to build model! INFO @ Fri, 26 Jun 2020 08:38:58: start model_add_line... INFO @ Fri, 26 Jun 2020 08:38:58: start X-correlation... INFO @ Fri, 26 Jun 2020 08:38:58: end of X-cor INFO @ Fri, 26 Jun 2020 08:38:58: #2 finished! INFO @ Fri, 26 Jun 2020 08:38:58: #2 predicted fragment length is 114 bps INFO @ Fri, 26 Jun 2020 08:38:58: #2 alternative fragment length(s) may be 114 bps INFO @ Fri, 26 Jun 2020 08:38:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1021226/SRX1021226.20_model.r INFO @ Fri, 26 Jun 2020 08:38:58: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:38:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:39:01: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:39:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1021226/SRX1021226.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:39:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1021226/SRX1021226.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:39:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1021226/SRX1021226.05_summits.bed INFO @ Fri, 26 Jun 2020 08:39:08: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2916 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:39:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1021226/SRX1021226.10_peaks.xls INFO @ Fri, 26 Jun 2020 08:39:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1021226/SRX1021226.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:39:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1021226/SRX1021226.10_summits.bed INFO @ Fri, 26 Jun 2020 08:39:14: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1455 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:39:24: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:39:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1021226/SRX1021226.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:39:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1021226/SRX1021226.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:39:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1021226/SRX1021226.20_summits.bed INFO @ Fri, 26 Jun 2020 08:39:38: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (811 records, 4 fields): 3 millis CompletedMACS2peakCalling