Job ID = 16438996 SRX = SRX15206439 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:20:52 prefetch.2.10.7: 1) Downloading 'SRR19139372'... 2022-08-02T05:20:52 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:21:05 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:21:05 prefetch.2.10.7: 'SRR19139372' is valid 2022-08-02T05:21:05 prefetch.2.10.7: 1) 'SRR19139372' was downloaded successfully 2022-08-02T05:21:05 prefetch.2.10.7: 'SRR19139372' has 0 unresolved dependencies Read 9069322 spots for SRR19139372/SRR19139372.sra Written 9069322 spots for SRR19139372/SRR19139372.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439125 ("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: 00:02:54 9069322 reads; of these: 9069322 (100.00%) were unpaired; of these: 319542 (3.52%) aligned 0 times 7892448 (87.02%) aligned exactly 1 time 857332 (9.45%) aligned >1 times 96.48% overall alignment rate Time searching: 00:02:54 Overall time: 00:02:54 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_rmdupse_core] 462881 / 8749780 = 0.0529 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 14:27:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206439/SRX15206439.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206439/SRX15206439.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206439/SRX15206439.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206439/SRX15206439.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 14:27:46: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:27:46: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:27:57: 1000000 INFO @ Tue, 02 Aug 2022 14:28:09: 2000000 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 14:28:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206439/SRX15206439.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206439/SRX15206439.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206439/SRX15206439.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206439/SRX15206439.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 14:28:16: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:28:16: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:28:21: 3000000 INFO @ Tue, 02 Aug 2022 14:28:27: 1000000 INFO @ Tue, 02 Aug 2022 14:28:32: 4000000 INFO @ Tue, 02 Aug 2022 14:28:39: 2000000 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 14:28:43: 5000000 INFO @ Tue, 02 Aug 2022 14:28:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206439/SRX15206439.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206439/SRX15206439.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206439/SRX15206439.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206439/SRX15206439.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 14:28:48: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:28:48: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:28:52: 3000000 INFO @ Tue, 02 Aug 2022 14:28:55: 6000000 INFO @ Tue, 02 Aug 2022 14:29:00: 1000000 INFO @ Tue, 02 Aug 2022 14:29:04: 4000000 INFO @ Tue, 02 Aug 2022 14:29:07: 7000000 INFO @ Tue, 02 Aug 2022 14:29:15: 2000000 INFO @ Tue, 02 Aug 2022 14:29:19: 5000000 INFO @ Tue, 02 Aug 2022 14:29:19: 8000000 INFO @ Tue, 02 Aug 2022 14:29:22: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:29:22: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:29:22: #1 total tags in treatment: 8286899 INFO @ Tue, 02 Aug 2022 14:29:22: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:29:22: #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 14:29:23: #1 tags after filtering in treatment: 8286899 INFO @ Tue, 02 Aug 2022 14:29:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:29:23: #1 finished! INFO @ Tue, 02 Aug 2022 14:29:23: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:29:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:29:23: #2 number of paired peaks: 121 WARNING @ Tue, 02 Aug 2022 14:29:23: Fewer paired peaks (121) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 121 pairs to build model! INFO @ Tue, 02 Aug 2022 14:29:23: start model_add_line... INFO @ Tue, 02 Aug 2022 14:29:24: start X-correlation... INFO @ Tue, 02 Aug 2022 14:29:24: end of X-cor INFO @ Tue, 02 Aug 2022 14:29:24: #2 finished! INFO @ Tue, 02 Aug 2022 14:29:24: #2 predicted fragment length is 191 bps INFO @ Tue, 02 Aug 2022 14:29:24: #2 alternative fragment length(s) may be 3,136,163,191,207,579 bps INFO @ Tue, 02 Aug 2022 14:29:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206439/SRX15206439.05_model.r INFO @ Tue, 02 Aug 2022 14:29:24: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:29:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:29:30: 3000000 INFO @ Tue, 02 Aug 2022 14:29:34: 6000000 INFO @ Tue, 02 Aug 2022 14:29:44: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:29:47: 7000000 INFO @ Tue, 02 Aug 2022 14:29:50: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:29:56: 5000000 INFO @ Tue, 02 Aug 2022 14:30:00: 8000000 INFO @ Tue, 02 Aug 2022 14:30:03: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:30:03: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:30:03: #1 total tags in treatment: 8286899 INFO @ Tue, 02 Aug 2022 14:30:03: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:30:03: #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 14:30:04: #1 tags after filtering in treatment: 8286899 INFO @ Tue, 02 Aug 2022 14:30:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:30:04: #1 finished! INFO @ Tue, 02 Aug 2022 14:30:04: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:30:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:30:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206439/SRX15206439.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:30:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206439/SRX15206439.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:30:04: #2 number of paired peaks: 121 WARNING @ Tue, 02 Aug 2022 14:30:04: Fewer paired peaks (121) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 121 pairs to build model! INFO @ Tue, 02 Aug 2022 14:30:04: start model_add_line... INFO @ Tue, 02 Aug 2022 14:30:04: start X-correlation... INFO @ Tue, 02 Aug 2022 14:30:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206439/SRX15206439.05_summits.bed INFO @ Tue, 02 Aug 2022 14:30:04: end of X-cor INFO @ Tue, 02 Aug 2022 14:30:04: #2 finished! INFO @ Tue, 02 Aug 2022 14:30:04: #2 predicted fragment length is 191 bps INFO @ Tue, 02 Aug 2022 14:30:04: #2 alternative fragment length(s) may be 3,136,163,191,207,579 bps INFO @ Tue, 02 Aug 2022 14:30:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206439/SRX15206439.10_model.r INFO @ Tue, 02 Aug 2022 14:30:04: Done! INFO @ Tue, 02 Aug 2022 14:30:04: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:30:04: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (647 records, 4 fields): 37 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:30:09: 6000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:30:20: 7000000 INFO @ Tue, 02 Aug 2022 14:30:30: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:30:31: 8000000 INFO @ Tue, 02 Aug 2022 14:30:34: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:30:34: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:30:34: #1 total tags in treatment: 8286899 INFO @ Tue, 02 Aug 2022 14:30:34: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:30:34: #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 14:30:34: #1 tags after filtering in treatment: 8286899 INFO @ Tue, 02 Aug 2022 14:30:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:30:34: #1 finished! INFO @ Tue, 02 Aug 2022 14:30:34: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:30:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:30:35: #2 number of paired peaks: 121 WARNING @ Tue, 02 Aug 2022 14:30:35: Fewer paired peaks (121) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 121 pairs to build model! INFO @ Tue, 02 Aug 2022 14:30:35: start model_add_line... INFO @ Tue, 02 Aug 2022 14:30:35: start X-correlation... INFO @ Tue, 02 Aug 2022 14:30:35: end of X-cor INFO @ Tue, 02 Aug 2022 14:30:35: #2 finished! INFO @ Tue, 02 Aug 2022 14:30:35: #2 predicted fragment length is 191 bps INFO @ Tue, 02 Aug 2022 14:30:35: #2 alternative fragment length(s) may be 3,136,163,191,207,579 bps INFO @ Tue, 02 Aug 2022 14:30:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206439/SRX15206439.20_model.r INFO @ Tue, 02 Aug 2022 14:30:35: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:30:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:30:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206439/SRX15206439.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:30:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206439/SRX15206439.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:30:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206439/SRX15206439.10_summits.bed INFO @ Tue, 02 Aug 2022 14:30:44: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (55 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:31:00: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:31:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206439/SRX15206439.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:31:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206439/SRX15206439.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:31:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206439/SRX15206439.20_summits.bed INFO @ Tue, 02 Aug 2022 14:31:14: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (19 records, 4 fields): 22 millis CompletedMACS2peakCalling