Job ID = 16438690 SRX = SRX15206503 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:03:50 prefetch.2.10.7: 1) Downloading 'SRR19139289'... 2022-08-02T05:03:50 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:04:12 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:04:13 prefetch.2.10.7: 'SRR19139289' is valid 2022-08-02T05:04:13 prefetch.2.10.7: 1) 'SRR19139289' was downloaded successfully 2022-08-02T05:04:13 prefetch.2.10.7: 'SRR19139289' has 0 unresolved dependencies Read 11927512 spots for SRR19139289/SRR19139289.sra Written 11927512 spots for SRR19139289/SRR19139289.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438937 ("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: 00:04:51 11927512 reads; of these: 11927512 (100.00%) were unpaired; of these: 379176 (3.18%) aligned 0 times 9680829 (81.16%) aligned exactly 1 time 1867507 (15.66%) aligned >1 times 96.82% overall alignment rate Time searching: 00:04:51 Overall time: 00:04:51 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 8 files... [bam_rmdupse_core] 556652 / 11548336 = 0.0482 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 14:14:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206503/SRX15206503.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206503/SRX15206503.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206503/SRX15206503.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206503/SRX15206503.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 14:14:28: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:14:28: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:14:34: 1000000 INFO @ Tue, 02 Aug 2022 14:14:40: 2000000 INFO @ Tue, 02 Aug 2022 14:14:47: 3000000 INFO @ Tue, 02 Aug 2022 14:14:53: 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 14:14:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206503/SRX15206503.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206503/SRX15206503.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206503/SRX15206503.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206503/SRX15206503.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 14:14:57: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:14:57: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:14:59: 5000000 INFO @ Tue, 02 Aug 2022 14:15:05: 1000000 INFO @ Tue, 02 Aug 2022 14:15:06: 6000000 INFO @ Tue, 02 Aug 2022 14:15:12: 7000000 INFO @ Tue, 02 Aug 2022 14:15:12: 2000000 INFO @ Tue, 02 Aug 2022 14:15:18: 8000000 INFO @ Tue, 02 Aug 2022 14:15:20: 3000000 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 14:15:25: 9000000 INFO @ Tue, 02 Aug 2022 14:15:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206503/SRX15206503.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206503/SRX15206503.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206503/SRX15206503.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206503/SRX15206503.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 14:15:27: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:15:27: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:15:28: 4000000 INFO @ Tue, 02 Aug 2022 14:15:32: 10000000 INFO @ Tue, 02 Aug 2022 14:15:36: 1000000 INFO @ Tue, 02 Aug 2022 14:15:36: 5000000 INFO @ Tue, 02 Aug 2022 14:15:40: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:15:40: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:15:40: #1 total tags in treatment: 10991684 INFO @ Tue, 02 Aug 2022 14:15:40: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:15:40: #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 14:15:40: #1 tags after filtering in treatment: 10991684 INFO @ Tue, 02 Aug 2022 14:15:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:15:40: #1 finished! INFO @ Tue, 02 Aug 2022 14:15:40: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:15:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:15:41: #2 number of paired peaks: 135 WARNING @ Tue, 02 Aug 2022 14:15:41: Fewer paired peaks (135) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 135 pairs to build model! INFO @ Tue, 02 Aug 2022 14:15:41: start model_add_line... INFO @ Tue, 02 Aug 2022 14:15:41: start X-correlation... INFO @ Tue, 02 Aug 2022 14:15:41: end of X-cor INFO @ Tue, 02 Aug 2022 14:15:41: #2 finished! INFO @ Tue, 02 Aug 2022 14:15:41: #2 predicted fragment length is 164 bps INFO @ Tue, 02 Aug 2022 14:15:41: #2 alternative fragment length(s) may be 3,69,102,114,129,164,550,577 bps INFO @ Tue, 02 Aug 2022 14:15:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206503/SRX15206503.05_model.r INFO @ Tue, 02 Aug 2022 14:15:41: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:15:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:15:44: 6000000 INFO @ Tue, 02 Aug 2022 14:15:44: 2000000 INFO @ Tue, 02 Aug 2022 14:15:52: 7000000 INFO @ Tue, 02 Aug 2022 14:15:53: 3000000 INFO @ Tue, 02 Aug 2022 14:15:59: 8000000 INFO @ Tue, 02 Aug 2022 14:16:01: 4000000 INFO @ Tue, 02 Aug 2022 14:16:01: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:16:07: 9000000 INFO @ Tue, 02 Aug 2022 14:16:09: 5000000 INFO @ Tue, 02 Aug 2022 14:16:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206503/SRX15206503.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:16:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206503/SRX15206503.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:16:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206503/SRX15206503.05_summits.bed INFO @ Tue, 02 Aug 2022 14:16:11: Done! pass1 - making usageList (12 chroms): 3 millis pass2 - checking and writing primary data (168 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:16:15: 10000000 INFO @ Tue, 02 Aug 2022 14:16:18: 6000000 INFO @ Tue, 02 Aug 2022 14:16:22: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:16:22: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:16:22: #1 total tags in treatment: 10991684 INFO @ Tue, 02 Aug 2022 14:16:22: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:16:22: #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 14:16:22: #1 tags after filtering in treatment: 10991684 INFO @ Tue, 02 Aug 2022 14:16:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:16:22: #1 finished! INFO @ Tue, 02 Aug 2022 14:16:22: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:16:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:16:23: #2 number of paired peaks: 135 WARNING @ Tue, 02 Aug 2022 14:16:23: Fewer paired peaks (135) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 135 pairs to build model! INFO @ Tue, 02 Aug 2022 14:16:23: start model_add_line... INFO @ Tue, 02 Aug 2022 14:16:23: start X-correlation... INFO @ Tue, 02 Aug 2022 14:16:23: end of X-cor INFO @ Tue, 02 Aug 2022 14:16:23: #2 finished! INFO @ Tue, 02 Aug 2022 14:16:23: #2 predicted fragment length is 164 bps INFO @ Tue, 02 Aug 2022 14:16:23: #2 alternative fragment length(s) may be 3,69,102,114,129,164,550,577 bps INFO @ Tue, 02 Aug 2022 14:16:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206503/SRX15206503.10_model.r INFO @ Tue, 02 Aug 2022 14:16:23: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:16:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:16:25: 7000000 INFO @ Tue, 02 Aug 2022 14:16:32: 8000000 INFO @ Tue, 02 Aug 2022 14:16:39: 9000000 INFO @ Tue, 02 Aug 2022 14:16:44: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:16:46: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:16:53: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:16:53: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:16:53: #1 total tags in treatment: 10991684 INFO @ Tue, 02 Aug 2022 14:16:53: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:16:53: #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 14:16:53: #1 tags after filtering in treatment: 10991684 INFO @ Tue, 02 Aug 2022 14:16:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:16:53: #1 finished! INFO @ Tue, 02 Aug 2022 14:16:53: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:16:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:16:54: #2 number of paired peaks: 135 WARNING @ Tue, 02 Aug 2022 14:16:54: Fewer paired peaks (135) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 135 pairs to build model! INFO @ Tue, 02 Aug 2022 14:16:54: start model_add_line... INFO @ Tue, 02 Aug 2022 14:16:54: start X-correlation... INFO @ Tue, 02 Aug 2022 14:16:54: end of X-cor INFO @ Tue, 02 Aug 2022 14:16:54: #2 finished! INFO @ Tue, 02 Aug 2022 14:16:54: #2 predicted fragment length is 164 bps INFO @ Tue, 02 Aug 2022 14:16:54: #2 alternative fragment length(s) may be 3,69,102,114,129,164,550,577 bps INFO @ Tue, 02 Aug 2022 14:16:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206503/SRX15206503.20_model.r INFO @ Tue, 02 Aug 2022 14:16:54: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:16:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:16:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206503/SRX15206503.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:16:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206503/SRX15206503.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:16:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206503/SRX15206503.10_summits.bed INFO @ Tue, 02 Aug 2022 14:16:54: Done! pass1 - making usageList (9 chroms): 2 millis pass2 - checking and writing primary data (77 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:17:14: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:17:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206503/SRX15206503.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:17:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206503/SRX15206503.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:17:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206503/SRX15206503.20_summits.bed INFO @ Tue, 02 Aug 2022 14:17:24: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (26 records, 4 fields): 34 millis CompletedMACS2peakCalling