Job ID = 14171028 SRX = SRX11704594 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2021-12-11T00:12:31 prefetch.2.10.7: 1) Downloading 'SRR15402378'... 2021-12-11T00:12:31 prefetch.2.10.7: Downloading via HTTPS... 2021-12-11T00:13:13 prefetch.2.10.7: HTTPS download succeed 2021-12-11T00:13:13 prefetch.2.10.7: 1) 'SRR15402378' was downloaded successfully 2021-12-11T00:13:13 prefetch.2.10.7: 'SRR15402378' has 0 unresolved dependencies Read 19763621 spots for SRR15402378/SRR15402378.sra Written 19763621 spots for SRR15402378/SRR15402378.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171505 ("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: 00:10:19 19763621 reads; of these: 19763621 (100.00%) were paired; of these: 7995731 (40.46%) aligned concordantly 0 times 10594058 (53.60%) aligned concordantly exactly 1 time 1173832 (5.94%) aligned concordantly >1 times ---- 7995731 pairs aligned concordantly 0 times; of these: 1298132 (16.24%) aligned discordantly 1 time ---- 6697599 pairs aligned 0 times concordantly or discordantly; of these: 13395198 mates make up the pairs; of these: 12145819 (90.67%) aligned 0 times 791614 (5.91%) aligned exactly 1 time 457765 (3.42%) aligned >1 times 69.27% overall alignment rate Time searching: 00:10:19 Overall time: 00:10:19 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] 2081137 / 12994081 = 0.1602 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 09:32:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11704594/SRX11704594.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11704594/SRX11704594.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11704594/SRX11704594.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11704594/SRX11704594.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 09:32:19: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:32:19: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:32:24: 1000000 INFO @ Sat, 11 Dec 2021 09:32:28: 2000000 INFO @ Sat, 11 Dec 2021 09:32:32: 3000000 INFO @ Sat, 11 Dec 2021 09:32:37: 4000000 INFO @ Sat, 11 Dec 2021 09:32:41: 5000000 INFO @ Sat, 11 Dec 2021 09:32:45: 6000000 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 09:32:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11704594/SRX11704594.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11704594/SRX11704594.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11704594/SRX11704594.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11704594/SRX11704594.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 09:32:49: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:32:49: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:32:50: 7000000 INFO @ Sat, 11 Dec 2021 09:32:54: 1000000 INFO @ Sat, 11 Dec 2021 09:32:54: 8000000 INFO @ Sat, 11 Dec 2021 09:32:58: 2000000 INFO @ Sat, 11 Dec 2021 09:32:59: 9000000 INFO @ Sat, 11 Dec 2021 09:33:03: 3000000 INFO @ Sat, 11 Dec 2021 09:33:03: 10000000 INFO @ Sat, 11 Dec 2021 09:33:08: 4000000 INFO @ Sat, 11 Dec 2021 09:33:08: 11000000 INFO @ Sat, 11 Dec 2021 09:33:12: 5000000 INFO @ Sat, 11 Dec 2021 09:33:13: 12000000 INFO @ Sat, 11 Dec 2021 09:33:17: 6000000 INFO @ Sat, 11 Dec 2021 09:33:17: 13000000 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 09:33:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11704594/SRX11704594.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11704594/SRX11704594.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11704594/SRX11704594.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11704594/SRX11704594.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 09:33:19: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:33:19: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:33:21: 7000000 INFO @ Sat, 11 Dec 2021 09:33:22: 14000000 INFO @ Sat, 11 Dec 2021 09:33:24: 1000000 INFO @ Sat, 11 Dec 2021 09:33:26: 8000000 INFO @ Sat, 11 Dec 2021 09:33:27: 15000000 INFO @ Sat, 11 Dec 2021 09:33:29: 2000000 INFO @ Sat, 11 Dec 2021 09:33:31: 9000000 INFO @ Sat, 11 Dec 2021 09:33:31: 16000000 INFO @ Sat, 11 Dec 2021 09:33:33: 3000000 INFO @ Sat, 11 Dec 2021 09:33:36: 10000000 INFO @ Sat, 11 Dec 2021 09:33:36: 17000000 INFO @ Sat, 11 Dec 2021 09:33:38: 4000000 INFO @ Sat, 11 Dec 2021 09:33:40: 11000000 INFO @ Sat, 11 Dec 2021 09:33:41: 18000000 INFO @ Sat, 11 Dec 2021 09:33:43: 5000000 INFO @ Sat, 11 Dec 2021 09:33:45: 12000000 INFO @ Sat, 11 Dec 2021 09:33:46: 19000000 INFO @ Sat, 11 Dec 2021 09:33:48: 6000000 INFO @ Sat, 11 Dec 2021 09:33:50: 13000000 INFO @ Sat, 11 Dec 2021 09:33:51: 20000000 INFO @ Sat, 11 Dec 2021 09:33:52: 7000000 INFO @ Sat, 11 Dec 2021 09:33:55: 14000000 INFO @ Sat, 11 Dec 2021 09:33:56: 21000000 INFO @ Sat, 11 Dec 2021 09:33:57: 8000000 INFO @ Sat, 11 Dec 2021 09:34:00: 15000000 INFO @ Sat, 11 Dec 2021 09:34:01: 22000000 INFO @ Sat, 11 Dec 2021 09:34:02: 9000000 INFO @ Sat, 11 Dec 2021 09:34:05: 16000000 INFO @ Sat, 11 Dec 2021 09:34:05: 23000000 INFO @ Sat, 11 Dec 2021 09:34:07: #1 tag size is determined as 35 bps INFO @ Sat, 11 Dec 2021 09:34:07: #1 tag size = 35 INFO @ Sat, 11 Dec 2021 09:34:07: #1 total tags in treatment: 9887558 INFO @ Sat, 11 Dec 2021 09:34:07: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:34:07: #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 09:34:07: 10000000 INFO @ Sat, 11 Dec 2021 09:34:07: #1 tags after filtering in treatment: 6136724 INFO @ Sat, 11 Dec 2021 09:34:07: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 11 Dec 2021 09:34:07: #1 finished! INFO @ Sat, 11 Dec 2021 09:34:07: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:34:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:34:07: #2 number of paired peaks: 6011 INFO @ Sat, 11 Dec 2021 09:34:08: start model_add_line... INFO @ Sat, 11 Dec 2021 09:34:08: start X-correlation... INFO @ Sat, 11 Dec 2021 09:34:08: end of X-cor INFO @ Sat, 11 Dec 2021 09:34:08: #2 finished! INFO @ Sat, 11 Dec 2021 09:34:08: #2 predicted fragment length is 100 bps INFO @ Sat, 11 Dec 2021 09:34:08: #2 alternative fragment length(s) may be 100 bps INFO @ Sat, 11 Dec 2021 09:34:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11704594/SRX11704594.05_model.r INFO @ Sat, 11 Dec 2021 09:34:08: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:34:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:34:10: 17000000 INFO @ Sat, 11 Dec 2021 09:34:11: 11000000 INFO @ Sat, 11 Dec 2021 09:34:14: 18000000 INFO @ Sat, 11 Dec 2021 09:34:16: 12000000 INFO @ Sat, 11 Dec 2021 09:34:19: 19000000 INFO @ Sat, 11 Dec 2021 09:34:21: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:34:21: 13000000 INFO @ Sat, 11 Dec 2021 09:34:24: 20000000 INFO @ Sat, 11 Dec 2021 09:34:26: 14000000 INFO @ Sat, 11 Dec 2021 09:34:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11704594/SRX11704594.05_peaks.xls INFO @ Sat, 11 Dec 2021 09:34:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11704594/SRX11704594.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:34:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11704594/SRX11704594.05_summits.bed INFO @ Sat, 11 Dec 2021 09:34:28: Done! INFO @ Sat, 11 Dec 2021 09:34:29: 21000000 pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (20044 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:34:30: 15000000 INFO @ Sat, 11 Dec 2021 09:34:33: 22000000 INFO @ Sat, 11 Dec 2021 09:34:35: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 09:34:38: 23000000 INFO @ Sat, 11 Dec 2021 09:34:39: #1 tag size is determined as 35 bps INFO @ Sat, 11 Dec 2021 09:34:39: #1 tag size = 35 INFO @ Sat, 11 Dec 2021 09:34:39: #1 total tags in treatment: 9887558 INFO @ Sat, 11 Dec 2021 09:34:39: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:34:39: #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 09:34:39: #1 tags after filtering in treatment: 6136724 INFO @ Sat, 11 Dec 2021 09:34:39: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 11 Dec 2021 09:34:39: #1 finished! INFO @ Sat, 11 Dec 2021 09:34:39: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:34:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:34:40: 17000000 INFO @ Sat, 11 Dec 2021 09:34:40: #2 number of paired peaks: 6011 INFO @ Sat, 11 Dec 2021 09:34:40: start model_add_line... INFO @ Sat, 11 Dec 2021 09:34:40: start X-correlation... INFO @ Sat, 11 Dec 2021 09:34:40: end of X-cor INFO @ Sat, 11 Dec 2021 09:34:40: #2 finished! INFO @ Sat, 11 Dec 2021 09:34:40: #2 predicted fragment length is 100 bps INFO @ Sat, 11 Dec 2021 09:34:40: #2 alternative fragment length(s) may be 100 bps INFO @ Sat, 11 Dec 2021 09:34:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11704594/SRX11704594.10_model.r INFO @ Sat, 11 Dec 2021 09:34:40: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:34:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:34:44: 18000000 INFO @ Sat, 11 Dec 2021 09:34:49: 19000000 INFO @ Sat, 11 Dec 2021 09:34:53: 20000000 INFO @ Sat, 11 Dec 2021 09:34:54: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:34:58: 21000000 INFO @ Sat, 11 Dec 2021 09:35:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11704594/SRX11704594.10_peaks.xls INFO @ Sat, 11 Dec 2021 09:35:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11704594/SRX11704594.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:35:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11704594/SRX11704594.10_summits.bed INFO @ Sat, 11 Dec 2021 09:35:01: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (13057 records, 4 fields): 13 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 09:35:02: 22000000 INFO @ Sat, 11 Dec 2021 09:35:07: 23000000 INFO @ Sat, 11 Dec 2021 09:35:08: #1 tag size is determined as 35 bps INFO @ Sat, 11 Dec 2021 09:35:08: #1 tag size = 35 INFO @ Sat, 11 Dec 2021 09:35:08: #1 total tags in treatment: 9887558 INFO @ Sat, 11 Dec 2021 09:35:08: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:35:08: #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 09:35:08: #1 tags after filtering in treatment: 6136724 INFO @ Sat, 11 Dec 2021 09:35:08: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 11 Dec 2021 09:35:08: #1 finished! INFO @ Sat, 11 Dec 2021 09:35:08: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:35:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:35:09: #2 number of paired peaks: 6011 INFO @ Sat, 11 Dec 2021 09:35:09: start model_add_line... INFO @ Sat, 11 Dec 2021 09:35:09: start X-correlation... INFO @ Sat, 11 Dec 2021 09:35:09: end of X-cor INFO @ Sat, 11 Dec 2021 09:35:09: #2 finished! INFO @ Sat, 11 Dec 2021 09:35:09: #2 predicted fragment length is 100 bps INFO @ Sat, 11 Dec 2021 09:35:09: #2 alternative fragment length(s) may be 100 bps INFO @ Sat, 11 Dec 2021 09:35:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11704594/SRX11704594.20_model.r INFO @ Sat, 11 Dec 2021 09:35:09: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:35:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:35:21: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:35:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11704594/SRX11704594.20_peaks.xls INFO @ Sat, 11 Dec 2021 09:35:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11704594/SRX11704594.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:35:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11704594/SRX11704594.20_summits.bed INFO @ Sat, 11 Dec 2021 09:35:28: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (6366 records, 4 fields): 7 millis CompletedMACS2peakCalling