Job ID = 16436935 SRX = SRX11638460 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T03:07:02 prefetch.2.10.7: 1) Downloading 'SRR15334169'... 2022-08-02T03:07:02 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T03:07:58 prefetch.2.10.7: HTTPS download succeed 2022-08-02T03:07:58 prefetch.2.10.7: 1) 'SRR15334169' was downloaded successfully 2022-08-02T03:07:58 prefetch.2.10.7: 'SRR15334169' has 0 unresolved dependencies Read 24432113 spots for SRR15334169/SRR15334169.sra Written 24432113 spots for SRR15334169/SRR15334169.sra fastq に変換しました。 bowtie でマッピング中... Your job 16437294 ("srTdm6") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:49 24432113 reads; of these: 24432113 (100.00%) were unpaired; of these: 1808332 (7.40%) aligned 0 times 19984417 (81.80%) aligned exactly 1 time 2639364 (10.80%) aligned >1 times 92.60% overall alignment rate Time searching: 00:06:50 Overall time: 00:06:50 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_rmdupse_core] 3126111 / 22623781 = 0.1382 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 12:21:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11638460/SRX11638460.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11638460/SRX11638460.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11638460/SRX11638460.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11638460/SRX11638460.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 12:21:40: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:21:40: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:21:46: 1000000 INFO @ Tue, 02 Aug 2022 12:21:53: 2000000 INFO @ Tue, 02 Aug 2022 12:21:59: 3000000 INFO @ Tue, 02 Aug 2022 12:22:05: 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 12:22:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11638460/SRX11638460.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11638460/SRX11638460.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11638460/SRX11638460.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11638460/SRX11638460.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 12:22:08: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:22:08: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:22:12: 5000000 INFO @ Tue, 02 Aug 2022 12:22:15: 1000000 INFO @ Tue, 02 Aug 2022 12:22:18: 6000000 INFO @ Tue, 02 Aug 2022 12:22:22: 2000000 INFO @ Tue, 02 Aug 2022 12:22:25: 7000000 INFO @ Tue, 02 Aug 2022 12:22:29: 3000000 INFO @ Tue, 02 Aug 2022 12:22:31: 8000000 INFO @ Tue, 02 Aug 2022 12:22:36: 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 12:22:38: 9000000 INFO @ Tue, 02 Aug 2022 12:22:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11638460/SRX11638460.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11638460/SRX11638460.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11638460/SRX11638460.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11638460/SRX11638460.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 12:22:38: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:22:38: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:22:43: 5000000 INFO @ Tue, 02 Aug 2022 12:22:44: 10000000 INFO @ Tue, 02 Aug 2022 12:22:45: 1000000 INFO @ Tue, 02 Aug 2022 12:22:50: 6000000 INFO @ Tue, 02 Aug 2022 12:22:50: 11000000 INFO @ Tue, 02 Aug 2022 12:22:52: 2000000 INFO @ Tue, 02 Aug 2022 12:22:57: 12000000 INFO @ Tue, 02 Aug 2022 12:22:57: 7000000 INFO @ Tue, 02 Aug 2022 12:22:59: 3000000 INFO @ Tue, 02 Aug 2022 12:23:03: 13000000 INFO @ Tue, 02 Aug 2022 12:23:04: 8000000 INFO @ Tue, 02 Aug 2022 12:23:06: 4000000 INFO @ Tue, 02 Aug 2022 12:23:09: 14000000 INFO @ Tue, 02 Aug 2022 12:23:11: 9000000 INFO @ Tue, 02 Aug 2022 12:23:12: 5000000 INFO @ Tue, 02 Aug 2022 12:23:16: 15000000 INFO @ Tue, 02 Aug 2022 12:23:18: 10000000 INFO @ Tue, 02 Aug 2022 12:23:19: 6000000 INFO @ Tue, 02 Aug 2022 12:23:22: 16000000 INFO @ Tue, 02 Aug 2022 12:23:25: 11000000 INFO @ Tue, 02 Aug 2022 12:23:26: 7000000 INFO @ Tue, 02 Aug 2022 12:23:28: 17000000 INFO @ Tue, 02 Aug 2022 12:23:32: 12000000 INFO @ Tue, 02 Aug 2022 12:23:32: 8000000 INFO @ Tue, 02 Aug 2022 12:23:34: 18000000 INFO @ Tue, 02 Aug 2022 12:23:38: 9000000 INFO @ Tue, 02 Aug 2022 12:23:39: 13000000 INFO @ Tue, 02 Aug 2022 12:23:41: 19000000 INFO @ Tue, 02 Aug 2022 12:23:44: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 12:23:44: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 12:23:44: #1 total tags in treatment: 19497670 INFO @ Tue, 02 Aug 2022 12:23:44: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:23:44: #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 12:23:44: #1 tags after filtering in treatment: 19497670 INFO @ Tue, 02 Aug 2022 12:23:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 12:23:44: #1 finished! INFO @ Tue, 02 Aug 2022 12:23:44: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:23:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:23:44: 10000000 INFO @ Tue, 02 Aug 2022 12:23:45: #2 number of paired peaks: 507 WARNING @ Tue, 02 Aug 2022 12:23:45: Fewer paired peaks (507) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 507 pairs to build model! INFO @ Tue, 02 Aug 2022 12:23:45: start model_add_line... INFO @ Tue, 02 Aug 2022 12:23:46: start X-correlation... INFO @ Tue, 02 Aug 2022 12:23:46: end of X-cor INFO @ Tue, 02 Aug 2022 12:23:46: #2 finished! INFO @ Tue, 02 Aug 2022 12:23:46: #2 predicted fragment length is 150 bps INFO @ Tue, 02 Aug 2022 12:23:46: #2 alternative fragment length(s) may be 150 bps INFO @ Tue, 02 Aug 2022 12:23:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11638460/SRX11638460.05_model.r INFO @ Tue, 02 Aug 2022 12:23:46: 14000000 INFO @ Tue, 02 Aug 2022 12:23:46: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:23:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:23:51: 11000000 INFO @ Tue, 02 Aug 2022 12:23:53: 15000000 INFO @ Tue, 02 Aug 2022 12:23:57: 12000000 INFO @ Tue, 02 Aug 2022 12:23:59: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 12:24:03: 13000000 INFO @ Tue, 02 Aug 2022 12:24:06: 17000000 INFO @ Tue, 02 Aug 2022 12:24:09: 14000000 INFO @ Tue, 02 Aug 2022 12:24:13: 18000000 INFO @ Tue, 02 Aug 2022 12:24:15: 15000000 INFO @ Tue, 02 Aug 2022 12:24:20: 19000000 INFO @ Tue, 02 Aug 2022 12:24:21: 16000000 INFO @ Tue, 02 Aug 2022 12:24:23: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 12:24:23: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 12:24:23: #1 total tags in treatment: 19497670 INFO @ Tue, 02 Aug 2022 12:24:23: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:24:23: #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 12:24:23: #1 tags after filtering in treatment: 19497670 INFO @ Tue, 02 Aug 2022 12:24:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 12:24:23: #1 finished! INFO @ Tue, 02 Aug 2022 12:24:23: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:24:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:24:25: #2 number of paired peaks: 507 WARNING @ Tue, 02 Aug 2022 12:24:25: Fewer paired peaks (507) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 507 pairs to build model! INFO @ Tue, 02 Aug 2022 12:24:25: start model_add_line... INFO @ Tue, 02 Aug 2022 12:24:25: start X-correlation... INFO @ Tue, 02 Aug 2022 12:24:25: end of X-cor INFO @ Tue, 02 Aug 2022 12:24:25: #2 finished! INFO @ Tue, 02 Aug 2022 12:24:25: #2 predicted fragment length is 150 bps INFO @ Tue, 02 Aug 2022 12:24:25: #2 alternative fragment length(s) may be 150 bps INFO @ Tue, 02 Aug 2022 12:24:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11638460/SRX11638460.10_model.r INFO @ Tue, 02 Aug 2022 12:24:25: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:24:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:24:26: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:24:27: 17000000 INFO @ Tue, 02 Aug 2022 12:24:33: 18000000 INFO @ Tue, 02 Aug 2022 12:24:38: 19000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 12:24:41: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 12:24:41: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 12:24:41: #1 total tags in treatment: 19497670 INFO @ Tue, 02 Aug 2022 12:24:41: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:24:41: #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 12:24:41: #1 tags after filtering in treatment: 19497670 INFO @ Tue, 02 Aug 2022 12:24:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 12:24:41: #1 finished! INFO @ Tue, 02 Aug 2022 12:24:41: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:24:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:24:43: #2 number of paired peaks: 507 WARNING @ Tue, 02 Aug 2022 12:24:43: Fewer paired peaks (507) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 507 pairs to build model! INFO @ Tue, 02 Aug 2022 12:24:43: start model_add_line... INFO @ Tue, 02 Aug 2022 12:24:43: start X-correlation... INFO @ Tue, 02 Aug 2022 12:24:43: end of X-cor INFO @ Tue, 02 Aug 2022 12:24:43: #2 finished! INFO @ Tue, 02 Aug 2022 12:24:43: #2 predicted fragment length is 150 bps INFO @ Tue, 02 Aug 2022 12:24:43: #2 alternative fragment length(s) may be 150 bps INFO @ Tue, 02 Aug 2022 12:24:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11638460/SRX11638460.20_model.r INFO @ Tue, 02 Aug 2022 12:24:43: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:24:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:24:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11638460/SRX11638460.05_peaks.xls INFO @ Tue, 02 Aug 2022 12:24:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11638460/SRX11638460.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:24:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11638460/SRX11638460.05_summits.bed INFO @ Tue, 02 Aug 2022 12:24:49: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (11332 records, 4 fields): 123 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 12:25:06: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:25:23: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:25:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11638460/SRX11638460.10_peaks.xls INFO @ Tue, 02 Aug 2022 12:25:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11638460/SRX11638460.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:25:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11638460/SRX11638460.10_summits.bed INFO @ Tue, 02 Aug 2022 12:25:30: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (7058 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 12:25:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11638460/SRX11638460.20_peaks.xls INFO @ Tue, 02 Aug 2022 12:25:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11638460/SRX11638460.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:25:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11638460/SRX11638460.20_summits.bed INFO @ Tue, 02 Aug 2022 12:25:45: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (3343 records, 4 fields): 25 millis CompletedMACS2peakCalling