Job ID = 14170475 SRX = SRX11472097 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2021-12-10T21:52:36 prefetch.2.10.7: 1) Downloading 'SRR15164745'... 2021-12-10T21:52:36 prefetch.2.10.7: Downloading via HTTPS... 2021-12-10T21:53:51 prefetch.2.10.7: HTTPS download succeed 2021-12-10T21:53:51 prefetch.2.10.7: 1) 'SRR15164745' was downloaded successfully 2021-12-10T21:53:51 prefetch.2.10.7: 'SRR15164745' has 0 unresolved dependencies Read 20511243 spots for SRR15164745/SRR15164745.sra Written 20511243 spots for SRR15164745/SRR15164745.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171019 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:39:29 20511243 reads; of these: 20511243 (100.00%) were paired; of these: 1484746 (7.24%) aligned concordantly 0 times 13459493 (65.62%) aligned concordantly exactly 1 time 5567004 (27.14%) aligned concordantly >1 times ---- 1484746 pairs aligned concordantly 0 times; of these: 300602 (20.25%) aligned discordantly 1 time ---- 1184144 pairs aligned 0 times concordantly or discordantly; of these: 2368288 mates make up the pairs; of these: 981630 (41.45%) aligned 0 times 757341 (31.98%) aligned exactly 1 time 629317 (26.57%) aligned >1 times 97.61% overall alignment rate Time searching: 00:39:29 Overall time: 00:39:29 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] 719887 / 19097783 = 0.0377 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 07:46:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11472097/SRX11472097.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11472097/SRX11472097.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11472097/SRX11472097.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11472097/SRX11472097.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 @ Sat, 11 Dec 2021 07:46:22: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:46:22: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:46:28: 1000000 INFO @ Sat, 11 Dec 2021 07:46:35: 2000000 INFO @ Sat, 11 Dec 2021 07:46:41: 3000000 INFO @ Sat, 11 Dec 2021 07:46:48: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 07:46:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11472097/SRX11472097.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11472097/SRX11472097.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11472097/SRX11472097.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11472097/SRX11472097.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 @ Sat, 11 Dec 2021 07:46:51: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:46:51: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:46:55: 5000000 INFO @ Sat, 11 Dec 2021 07:46:58: 1000000 INFO @ Sat, 11 Dec 2021 07:47:02: 6000000 INFO @ Sat, 11 Dec 2021 07:47:04: 2000000 INFO @ Sat, 11 Dec 2021 07:47:10: 7000000 INFO @ Sat, 11 Dec 2021 07:47:10: 3000000 INFO @ Sat, 11 Dec 2021 07:47:17: 4000000 INFO @ Sat, 11 Dec 2021 07:47:17: 8000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 07:47:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11472097/SRX11472097.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11472097/SRX11472097.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11472097/SRX11472097.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11472097/SRX11472097.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 @ Sat, 11 Dec 2021 07:47:21: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:47:21: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:47:23: 5000000 INFO @ Sat, 11 Dec 2021 07:47:25: 9000000 INFO @ Sat, 11 Dec 2021 07:47:29: 1000000 INFO @ Sat, 11 Dec 2021 07:47:29: 6000000 INFO @ Sat, 11 Dec 2021 07:47:32: 10000000 INFO @ Sat, 11 Dec 2021 07:47:36: 7000000 INFO @ Sat, 11 Dec 2021 07:47:36: 2000000 INFO @ Sat, 11 Dec 2021 07:47:39: 11000000 INFO @ Sat, 11 Dec 2021 07:47:42: 8000000 INFO @ Sat, 11 Dec 2021 07:47:44: 3000000 INFO @ Sat, 11 Dec 2021 07:47:47: 12000000 INFO @ Sat, 11 Dec 2021 07:47:48: 9000000 INFO @ Sat, 11 Dec 2021 07:47:51: 4000000 INFO @ Sat, 11 Dec 2021 07:47:54: 13000000 INFO @ Sat, 11 Dec 2021 07:47:55: 10000000 INFO @ Sat, 11 Dec 2021 07:47:58: 5000000 INFO @ Sat, 11 Dec 2021 07:48:01: 11000000 INFO @ Sat, 11 Dec 2021 07:48:02: 14000000 INFO @ Sat, 11 Dec 2021 07:48:06: 6000000 INFO @ Sat, 11 Dec 2021 07:48:08: 12000000 INFO @ Sat, 11 Dec 2021 07:48:09: 15000000 INFO @ Sat, 11 Dec 2021 07:48:13: 7000000 INFO @ Sat, 11 Dec 2021 07:48:14: 13000000 INFO @ Sat, 11 Dec 2021 07:48:17: 16000000 INFO @ Sat, 11 Dec 2021 07:48:20: 8000000 INFO @ Sat, 11 Dec 2021 07:48:21: 14000000 INFO @ Sat, 11 Dec 2021 07:48:24: 17000000 INFO @ Sat, 11 Dec 2021 07:48:27: 15000000 INFO @ Sat, 11 Dec 2021 07:48:28: 9000000 INFO @ Sat, 11 Dec 2021 07:48:32: 18000000 INFO @ Sat, 11 Dec 2021 07:48:34: 16000000 INFO @ Sat, 11 Dec 2021 07:48:35: 10000000 INFO @ Sat, 11 Dec 2021 07:48:39: 19000000 INFO @ Sat, 11 Dec 2021 07:48:40: 17000000 INFO @ Sat, 11 Dec 2021 07:48:42: 11000000 INFO @ Sat, 11 Dec 2021 07:48:46: 18000000 INFO @ Sat, 11 Dec 2021 07:48:47: 20000000 INFO @ Sat, 11 Dec 2021 07:48:50: 12000000 INFO @ Sat, 11 Dec 2021 07:48:53: 19000000 INFO @ Sat, 11 Dec 2021 07:48:54: 21000000 INFO @ Sat, 11 Dec 2021 07:48:57: 13000000 INFO @ Sat, 11 Dec 2021 07:48:59: 20000000 INFO @ Sat, 11 Dec 2021 07:49:02: 22000000 INFO @ Sat, 11 Dec 2021 07:49:05: 14000000 INFO @ Sat, 11 Dec 2021 07:49:05: 21000000 INFO @ Sat, 11 Dec 2021 07:49:09: 23000000 INFO @ Sat, 11 Dec 2021 07:49:12: 22000000 INFO @ Sat, 11 Dec 2021 07:49:12: 15000000 INFO @ Sat, 11 Dec 2021 07:49:16: 24000000 INFO @ Sat, 11 Dec 2021 07:49:18: 23000000 INFO @ Sat, 11 Dec 2021 07:49:19: 16000000 INFO @ Sat, 11 Dec 2021 07:49:24: 25000000 INFO @ Sat, 11 Dec 2021 07:49:25: 24000000 INFO @ Sat, 11 Dec 2021 07:49:27: 17000000 INFO @ Sat, 11 Dec 2021 07:49:31: 25000000 INFO @ Sat, 11 Dec 2021 07:49:31: 26000000 INFO @ Sat, 11 Dec 2021 07:49:34: 18000000 INFO @ Sat, 11 Dec 2021 07:49:37: 26000000 INFO @ Sat, 11 Dec 2021 07:49:39: 27000000 INFO @ Sat, 11 Dec 2021 07:49:41: 19000000 INFO @ Sat, 11 Dec 2021 07:49:44: 27000000 INFO @ Sat, 11 Dec 2021 07:49:46: 28000000 INFO @ Sat, 11 Dec 2021 07:49:49: 20000000 INFO @ Sat, 11 Dec 2021 07:49:50: 28000000 INFO @ Sat, 11 Dec 2021 07:49:54: 29000000 INFO @ Sat, 11 Dec 2021 07:49:56: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 07:49:57: 29000000 INFO @ Sat, 11 Dec 2021 07:50:01: 30000000 INFO @ Sat, 11 Dec 2021 07:50:03: 30000000 INFO @ Sat, 11 Dec 2021 07:50:03: 22000000 INFO @ Sat, 11 Dec 2021 07:50:09: 31000000 INFO @ Sat, 11 Dec 2021 07:50:10: 31000000 INFO @ Sat, 11 Dec 2021 07:50:11: 23000000 INFO @ Sat, 11 Dec 2021 07:50:16: 32000000 INFO @ Sat, 11 Dec 2021 07:50:17: 32000000 INFO @ Sat, 11 Dec 2021 07:50:18: 24000000 INFO @ Sat, 11 Dec 2021 07:50:24: 33000000 INFO @ Sat, 11 Dec 2021 07:50:24: 33000000 INFO @ Sat, 11 Dec 2021 07:50:26: 25000000 INFO @ Sat, 11 Dec 2021 07:50:31: 34000000 INFO @ Sat, 11 Dec 2021 07:50:32: 34000000 INFO @ Sat, 11 Dec 2021 07:50:33: 26000000 INFO @ Sat, 11 Dec 2021 07:50:39: 35000000 INFO @ Sat, 11 Dec 2021 07:50:39: 35000000 INFO @ Sat, 11 Dec 2021 07:50:40: 27000000 INFO @ Sat, 11 Dec 2021 07:50:46: 36000000 INFO @ Sat, 11 Dec 2021 07:50:47: 36000000 INFO @ Sat, 11 Dec 2021 07:50:48: 28000000 INFO @ Sat, 11 Dec 2021 07:50:54: 37000000 INFO @ Sat, 11 Dec 2021 07:50:54: 37000000 INFO @ Sat, 11 Dec 2021 07:50:55: 29000000 INFO @ Sat, 11 Dec 2021 07:51:01: 38000000 INFO @ Sat, 11 Dec 2021 07:51:02: 38000000 INFO @ Sat, 11 Dec 2021 07:51:02: 30000000 INFO @ Sat, 11 Dec 2021 07:51:06: #1 tag size is determined as 51 bps INFO @ Sat, 11 Dec 2021 07:51:06: #1 tag size = 51 INFO @ Sat, 11 Dec 2021 07:51:06: #1 total tags in treatment: 18308701 INFO @ Sat, 11 Dec 2021 07:51:06: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:51:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 07:51:06: #1 tags after filtering in treatment: 16590272 INFO @ Sat, 11 Dec 2021 07:51:06: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 11 Dec 2021 07:51:06: #1 finished! INFO @ Sat, 11 Dec 2021 07:51:06: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:51:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:51:06: #1 tag size is determined as 51 bps INFO @ Sat, 11 Dec 2021 07:51:06: #1 tag size = 51 INFO @ Sat, 11 Dec 2021 07:51:06: #1 total tags in treatment: 18308701 INFO @ Sat, 11 Dec 2021 07:51:06: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:51:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 07:51:07: #1 tags after filtering in treatment: 16590272 INFO @ Sat, 11 Dec 2021 07:51:07: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 11 Dec 2021 07:51:07: #1 finished! INFO @ Sat, 11 Dec 2021 07:51:07: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:51:07: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 07:51:07: #2 number of paired peaks: 958 WARNING @ Sat, 11 Dec 2021 07:51:07: Fewer paired peaks (958) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 958 pairs to build model! INFO @ Sat, 11 Dec 2021 07:51:07: start model_add_line... INFO @ Sat, 11 Dec 2021 07:51:07: start X-correlation... INFO @ Sat, 11 Dec 2021 07:51:07: end of X-cor INFO @ Sat, 11 Dec 2021 07:51:07: #2 finished! INFO @ Sat, 11 Dec 2021 07:51:07: #2 predicted fragment length is 173 bps INFO @ Sat, 11 Dec 2021 07:51:07: #2 alternative fragment length(s) may be 173 bps INFO @ Sat, 11 Dec 2021 07:51:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11472097/SRX11472097.05_model.r INFO @ Sat, 11 Dec 2021 07:51:07: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:51:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:51:08: #2 number of paired peaks: 958 WARNING @ Sat, 11 Dec 2021 07:51:08: Fewer paired peaks (958) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 958 pairs to build model! INFO @ Sat, 11 Dec 2021 07:51:08: start model_add_line... INFO @ Sat, 11 Dec 2021 07:51:08: start X-correlation... INFO @ Sat, 11 Dec 2021 07:51:08: end of X-cor INFO @ Sat, 11 Dec 2021 07:51:08: #2 finished! INFO @ Sat, 11 Dec 2021 07:51:08: #2 predicted fragment length is 173 bps INFO @ Sat, 11 Dec 2021 07:51:08: #2 alternative fragment length(s) may be 173 bps INFO @ Sat, 11 Dec 2021 07:51:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11472097/SRX11472097.10_model.r INFO @ Sat, 11 Dec 2021 07:51:08: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:51:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:51:10: 31000000 INFO @ Sat, 11 Dec 2021 07:51:16: 32000000 INFO @ Sat, 11 Dec 2021 07:51:23: 33000000 INFO @ Sat, 11 Dec 2021 07:51:29: 34000000 INFO @ Sat, 11 Dec 2021 07:51:36: 35000000 INFO @ Sat, 11 Dec 2021 07:51:41: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:51:42: 36000000 INFO @ Sat, 11 Dec 2021 07:51:42: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:51:49: 37000000 INFO @ Sat, 11 Dec 2021 07:51:55: 38000000 INFO @ Sat, 11 Dec 2021 07:51:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11472097/SRX11472097.05_peaks.xls INFO @ Sat, 11 Dec 2021 07:51:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11472097/SRX11472097.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:51:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11472097/SRX11472097.05_summits.bed INFO @ Sat, 11 Dec 2021 07:51:57: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3838 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:51:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11472097/SRX11472097.10_peaks.xls INFO @ Sat, 11 Dec 2021 07:51:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11472097/SRX11472097.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:51:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11472097/SRX11472097.10_summits.bed INFO @ Sat, 11 Dec 2021 07:51:58: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2279 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:51:59: #1 tag size is determined as 51 bps INFO @ Sat, 11 Dec 2021 07:51:59: #1 tag size = 51 INFO @ Sat, 11 Dec 2021 07:51:59: #1 total tags in treatment: 18308701 INFO @ Sat, 11 Dec 2021 07:51:59: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:51:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 07:52:00: #1 tags after filtering in treatment: 16590272 INFO @ Sat, 11 Dec 2021 07:52:00: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 11 Dec 2021 07:52:00: #1 finished! INFO @ Sat, 11 Dec 2021 07:52:00: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:52:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:52:01: #2 number of paired peaks: 958 WARNING @ Sat, 11 Dec 2021 07:52:01: Fewer paired peaks (958) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 958 pairs to build model! INFO @ Sat, 11 Dec 2021 07:52:01: start model_add_line... INFO @ Sat, 11 Dec 2021 07:52:01: start X-correlation... INFO @ Sat, 11 Dec 2021 07:52:01: end of X-cor INFO @ Sat, 11 Dec 2021 07:52:01: #2 finished! INFO @ Sat, 11 Dec 2021 07:52:01: #2 predicted fragment length is 173 bps INFO @ Sat, 11 Dec 2021 07:52:01: #2 alternative fragment length(s) may be 173 bps INFO @ Sat, 11 Dec 2021 07:52:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11472097/SRX11472097.20_model.r INFO @ Sat, 11 Dec 2021 07:52:01: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:52:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:52:36: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:52:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11472097/SRX11472097.20_peaks.xls INFO @ Sat, 11 Dec 2021 07:52:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11472097/SRX11472097.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:52:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11472097/SRX11472097.20_summits.bed INFO @ Sat, 11 Dec 2021 07:52:51: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1061 records, 4 fields): 5 millis CompletedMACS2peakCalling