Job ID = 16436544 SRX = SRX11638456 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T02:38:13 prefetch.2.10.7: 1) Downloading 'SRR15334165'... 2022-08-02T02:38:13 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T02:39:02 prefetch.2.10.7: HTTPS download succeed 2022-08-02T02:39:02 prefetch.2.10.7: 1) 'SRR15334165' was downloaded successfully 2022-08-02T02:39:02 prefetch.2.10.7: 'SRR15334165' has 0 unresolved dependencies Read 22812969 spots for SRR15334165/SRR15334165.sra Written 22812969 spots for SRR15334165/SRR15334165.sra fastq に変換しました。 bowtie でマッピング中... Your job 16436809 ("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: 00:05:17 22812969 reads; of these: 22812969 (100.00%) were unpaired; of these: 1861916 (8.16%) aligned 0 times 19521316 (85.57%) aligned exactly 1 time 1429737 (6.27%) aligned >1 times 91.84% overall alignment rate Time searching: 00:05:17 Overall time: 00:05:17 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_rmdupse_core] 4407942 / 20951053 = 0.2104 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 11:50:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11638456/SRX11638456.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11638456/SRX11638456.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11638456/SRX11638456.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11638456/SRX11638456.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 @ Tue, 02 Aug 2022 11:50:23: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:50:23: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:50:28: 1000000 INFO @ Tue, 02 Aug 2022 11:50:34: 2000000 INFO @ Tue, 02 Aug 2022 11:50:40: 3000000 INFO @ Tue, 02 Aug 2022 11:50:45: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 11:50:51: 5000000 INFO @ Tue, 02 Aug 2022 11:50:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11638456/SRX11638456.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11638456/SRX11638456.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11638456/SRX11638456.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11638456/SRX11638456.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 @ Tue, 02 Aug 2022 11:50:53: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:50:53: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:50:57: 6000000 INFO @ Tue, 02 Aug 2022 11:50:59: 1000000 INFO @ Tue, 02 Aug 2022 11:51:03: 7000000 INFO @ Tue, 02 Aug 2022 11:51:05: 2000000 INFO @ Tue, 02 Aug 2022 11:51:09: 8000000 INFO @ Tue, 02 Aug 2022 11:51:10: 3000000 INFO @ Tue, 02 Aug 2022 11:51:15: 9000000 INFO @ Tue, 02 Aug 2022 11:51:16: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 11:51:21: 10000000 INFO @ Tue, 02 Aug 2022 11:51:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11638456/SRX11638456.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11638456/SRX11638456.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11638456/SRX11638456.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11638456/SRX11638456.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 @ Tue, 02 Aug 2022 11:51:22: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:51:22: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:51:22: 5000000 INFO @ Tue, 02 Aug 2022 11:51:27: 11000000 INFO @ Tue, 02 Aug 2022 11:51:29: 6000000 INFO @ Tue, 02 Aug 2022 11:51:29: 1000000 INFO @ Tue, 02 Aug 2022 11:51:34: 12000000 INFO @ Tue, 02 Aug 2022 11:51:35: 7000000 INFO @ Tue, 02 Aug 2022 11:51:36: 2000000 INFO @ Tue, 02 Aug 2022 11:51:40: 13000000 INFO @ Tue, 02 Aug 2022 11:51:42: 8000000 INFO @ Tue, 02 Aug 2022 11:51:43: 3000000 INFO @ Tue, 02 Aug 2022 11:51:47: 14000000 INFO @ Tue, 02 Aug 2022 11:51:48: 9000000 INFO @ Tue, 02 Aug 2022 11:51:50: 4000000 INFO @ Tue, 02 Aug 2022 11:51:53: 15000000 INFO @ Tue, 02 Aug 2022 11:51:55: 10000000 INFO @ Tue, 02 Aug 2022 11:51:57: 5000000 INFO @ Tue, 02 Aug 2022 11:52:00: 16000000 INFO @ Tue, 02 Aug 2022 11:52:01: 11000000 INFO @ Tue, 02 Aug 2022 11:52:03: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 11:52:03: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 11:52:03: #1 total tags in treatment: 16543111 INFO @ Tue, 02 Aug 2022 11:52:03: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:52:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 11:52:04: #1 tags after filtering in treatment: 16543111 INFO @ Tue, 02 Aug 2022 11:52:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:52:04: #1 finished! INFO @ Tue, 02 Aug 2022 11:52:04: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:52:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:52:04: 6000000 INFO @ Tue, 02 Aug 2022 11:52:05: #2 number of paired peaks: 4577 INFO @ Tue, 02 Aug 2022 11:52:05: start model_add_line... INFO @ Tue, 02 Aug 2022 11:52:05: start X-correlation... INFO @ Tue, 02 Aug 2022 11:52:05: end of X-cor INFO @ Tue, 02 Aug 2022 11:52:05: #2 finished! INFO @ Tue, 02 Aug 2022 11:52:05: #2 predicted fragment length is 171 bps INFO @ Tue, 02 Aug 2022 11:52:05: #2 alternative fragment length(s) may be 171 bps INFO @ Tue, 02 Aug 2022 11:52:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11638456/SRX11638456.05_model.r INFO @ Tue, 02 Aug 2022 11:52:06: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:52:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:52:07: 12000000 INFO @ Tue, 02 Aug 2022 11:52:11: 7000000 INFO @ Tue, 02 Aug 2022 11:52:14: 13000000 INFO @ Tue, 02 Aug 2022 11:52:18: 8000000 INFO @ Tue, 02 Aug 2022 11:52:20: 14000000 INFO @ Tue, 02 Aug 2022 11:52:25: 9000000 INFO @ Tue, 02 Aug 2022 11:52:26: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 11:52:32: 10000000 INFO @ Tue, 02 Aug 2022 11:52:33: 16000000 INFO @ Tue, 02 Aug 2022 11:52:36: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 11:52:36: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 11:52:36: #1 total tags in treatment: 16543111 INFO @ Tue, 02 Aug 2022 11:52:36: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:52:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 11:52:36: #1 tags after filtering in treatment: 16543111 INFO @ Tue, 02 Aug 2022 11:52:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:52:36: #1 finished! INFO @ Tue, 02 Aug 2022 11:52:36: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:52:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:52:38: #2 number of paired peaks: 4577 INFO @ Tue, 02 Aug 2022 11:52:38: start model_add_line... INFO @ Tue, 02 Aug 2022 11:52:38: start X-correlation... INFO @ Tue, 02 Aug 2022 11:52:38: end of X-cor INFO @ Tue, 02 Aug 2022 11:52:38: #2 finished! INFO @ Tue, 02 Aug 2022 11:52:38: #2 predicted fragment length is 171 bps INFO @ Tue, 02 Aug 2022 11:52:38: #2 alternative fragment length(s) may be 171 bps INFO @ Tue, 02 Aug 2022 11:52:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11638456/SRX11638456.10_model.r INFO @ Tue, 02 Aug 2022 11:52:39: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:52:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:52:39: 11000000 INFO @ Tue, 02 Aug 2022 11:52:44: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:52:45: 12000000 INFO @ Tue, 02 Aug 2022 11:52:52: 13000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 11:52:59: 14000000 INFO @ Tue, 02 Aug 2022 11:53:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11638456/SRX11638456.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:53:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11638456/SRX11638456.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:53:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11638456/SRX11638456.05_summits.bed INFO @ Tue, 02 Aug 2022 11:53:04: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (14919 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:53:05: 15000000 INFO @ Tue, 02 Aug 2022 11:53:12: 16000000 INFO @ Tue, 02 Aug 2022 11:53:15: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 11:53:15: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 11:53:15: #1 total tags in treatment: 16543111 INFO @ Tue, 02 Aug 2022 11:53:15: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:53:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 11:53:15: #1 tags after filtering in treatment: 16543111 INFO @ Tue, 02 Aug 2022 11:53:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:53:15: #1 finished! INFO @ Tue, 02 Aug 2022 11:53:15: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:53:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:53:17: #2 number of paired peaks: 4577 INFO @ Tue, 02 Aug 2022 11:53:17: start model_add_line... INFO @ Tue, 02 Aug 2022 11:53:17: start X-correlation... INFO @ Tue, 02 Aug 2022 11:53:17: end of X-cor INFO @ Tue, 02 Aug 2022 11:53:17: #2 finished! INFO @ Tue, 02 Aug 2022 11:53:17: #2 predicted fragment length is 171 bps INFO @ Tue, 02 Aug 2022 11:53:17: #2 alternative fragment length(s) may be 171 bps INFO @ Tue, 02 Aug 2022 11:53:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11638456/SRX11638456.20_model.r INFO @ Tue, 02 Aug 2022 11:53:17: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:53:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:53:18: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:53:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11638456/SRX11638456.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:53:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11638456/SRX11638456.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:53:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11638456/SRX11638456.10_summits.bed INFO @ Tue, 02 Aug 2022 11:53:38: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (11527 records, 4 fields): 65 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:53:55: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:54:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11638456/SRX11638456.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:54:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11638456/SRX11638456.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:54:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11638456/SRX11638456.20_summits.bed INFO @ Tue, 02 Aug 2022 11:54:13: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (7875 records, 4 fields): 33 millis CompletedMACS2peakCalling