Job ID = 16438702 SRX = SRX15206511 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:06:56 prefetch.2.10.7: 1) Downloading 'SRR19139281'... 2022-08-02T05:06:56 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:07:14 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:07:15 prefetch.2.10.7: 'SRR19139281' is valid 2022-08-02T05:07:15 prefetch.2.10.7: 1) 'SRR19139281' was downloaded successfully 2022-08-02T05:07:15 prefetch.2.10.7: 'SRR19139281' has 0 unresolved dependencies Read 14217417 spots for SRR19139281/SRR19139281.sra Written 14217417 spots for SRR19139281/SRR19139281.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438951 ("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: 00:03:58 14217417 reads; of these: 14217417 (100.00%) were unpaired; of these: 1674904 (11.78%) aligned 0 times 8864001 (62.35%) aligned exactly 1 time 3678512 (25.87%) aligned >1 times 88.22% overall alignment rate Time searching: 00:03:58 Overall time: 00:03:58 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] 3812607 / 12542513 = 0.3040 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 14:15:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206511/SRX15206511.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206511/SRX15206511.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206511/SRX15206511.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206511/SRX15206511.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 14:15:20: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:15:20: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:15:25: 1000000 INFO @ Tue, 02 Aug 2022 14:15:31: 2000000 INFO @ Tue, 02 Aug 2022 14:15:36: 3000000 INFO @ Tue, 02 Aug 2022 14:15:42: 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 14:15:48: 5000000 INFO @ Tue, 02 Aug 2022 14:15:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206511/SRX15206511.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206511/SRX15206511.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206511/SRX15206511.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206511/SRX15206511.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 14:15:48: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:15:48: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:15:54: 6000000 INFO @ Tue, 02 Aug 2022 14:15:55: 1000000 INFO @ Tue, 02 Aug 2022 14:16:00: 7000000 INFO @ Tue, 02 Aug 2022 14:16:01: 2000000 INFO @ Tue, 02 Aug 2022 14:16:07: 8000000 INFO @ Tue, 02 Aug 2022 14:16:08: 3000000 INFO @ Tue, 02 Aug 2022 14:16:12: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:16:12: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:16:12: #1 total tags in treatment: 8729906 INFO @ Tue, 02 Aug 2022 14:16:12: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:16:12: #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 14:16:12: #1 tags after filtering in treatment: 8729906 INFO @ Tue, 02 Aug 2022 14:16:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:16:12: #1 finished! INFO @ Tue, 02 Aug 2022 14:16:12: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:16:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:16:13: #2 number of paired peaks: 532 WARNING @ Tue, 02 Aug 2022 14:16:13: Fewer paired peaks (532) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 532 pairs to build model! INFO @ Tue, 02 Aug 2022 14:16:13: start model_add_line... INFO @ Tue, 02 Aug 2022 14:16:13: start X-correlation... INFO @ Tue, 02 Aug 2022 14:16:13: end of X-cor INFO @ Tue, 02 Aug 2022 14:16:13: #2 finished! INFO @ Tue, 02 Aug 2022 14:16:13: #2 predicted fragment length is 154 bps INFO @ Tue, 02 Aug 2022 14:16:13: #2 alternative fragment length(s) may be 154 bps INFO @ Tue, 02 Aug 2022 14:16:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206511/SRX15206511.05_model.r INFO @ Tue, 02 Aug 2022 14:16:13: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:16:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:16:14: 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 14:16:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206511/SRX15206511.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206511/SRX15206511.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206511/SRX15206511.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206511/SRX15206511.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 14:16:19: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:16:19: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:16:21: 5000000 INFO @ Tue, 02 Aug 2022 14:16:26: 1000000 INFO @ Tue, 02 Aug 2022 14:16:27: 6000000 INFO @ Tue, 02 Aug 2022 14:16:31: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:16:32: 2000000 INFO @ Tue, 02 Aug 2022 14:16:33: 7000000 INFO @ Tue, 02 Aug 2022 14:16:38: 3000000 INFO @ Tue, 02 Aug 2022 14:16:40: 8000000 INFO @ Tue, 02 Aug 2022 14:16:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206511/SRX15206511.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:16:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206511/SRX15206511.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:16:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206511/SRX15206511.05_summits.bed INFO @ Tue, 02 Aug 2022 14:16:40: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2545 records, 4 fields): 48 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:16:44: 4000000 INFO @ Tue, 02 Aug 2022 14:16:44: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:16:44: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:16:44: #1 total tags in treatment: 8729906 INFO @ Tue, 02 Aug 2022 14:16:44: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:16:44: #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 14:16:44: #1 tags after filtering in treatment: 8729906 INFO @ Tue, 02 Aug 2022 14:16:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:16:44: #1 finished! INFO @ Tue, 02 Aug 2022 14:16:44: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:16:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:16:45: #2 number of paired peaks: 532 WARNING @ Tue, 02 Aug 2022 14:16:45: Fewer paired peaks (532) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 532 pairs to build model! INFO @ Tue, 02 Aug 2022 14:16:45: start model_add_line... INFO @ Tue, 02 Aug 2022 14:16:45: start X-correlation... INFO @ Tue, 02 Aug 2022 14:16:45: end of X-cor INFO @ Tue, 02 Aug 2022 14:16:45: #2 finished! INFO @ Tue, 02 Aug 2022 14:16:45: #2 predicted fragment length is 154 bps INFO @ Tue, 02 Aug 2022 14:16:45: #2 alternative fragment length(s) may be 154 bps INFO @ Tue, 02 Aug 2022 14:16:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206511/SRX15206511.10_model.r INFO @ Tue, 02 Aug 2022 14:16:45: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:16:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:16:49: 5000000 INFO @ Tue, 02 Aug 2022 14:16:55: 6000000 INFO @ Tue, 02 Aug 2022 14:17:01: 7000000 INFO @ Tue, 02 Aug 2022 14:17:02: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:17:07: 8000000 INFO @ Tue, 02 Aug 2022 14:17:11: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:17:11: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:17:11: #1 total tags in treatment: 8729906 INFO @ Tue, 02 Aug 2022 14:17:11: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:17:11: #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 14:17:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206511/SRX15206511.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:17:11: #1 tags after filtering in treatment: 8729906 INFO @ Tue, 02 Aug 2022 14:17:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:17:11: #1 finished! INFO @ Tue, 02 Aug 2022 14:17:11: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:17:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:17:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206511/SRX15206511.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:17:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206511/SRX15206511.10_summits.bed INFO @ Tue, 02 Aug 2022 14:17:11: Done! pass1 - making usageList (14 chroms): 1 millis INFO @ Tue, 02 Aug 2022 14:17:12: #2 number of paired peaks: 532 WARNING @ Tue, 02 Aug 2022 14:17:12: Fewer paired peaks (532) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 532 pairs to build model! INFO @ Tue, 02 Aug 2022 14:17:12: start model_add_line... pass2 - checking and writing primary data (1142 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:17:12: start X-correlation... INFO @ Tue, 02 Aug 2022 14:17:12: end of X-cor INFO @ Tue, 02 Aug 2022 14:17:12: #2 finished! INFO @ Tue, 02 Aug 2022 14:17:12: #2 predicted fragment length is 154 bps INFO @ Tue, 02 Aug 2022 14:17:12: #2 alternative fragment length(s) may be 154 bps INFO @ Tue, 02 Aug 2022 14:17:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206511/SRX15206511.20_model.r INFO @ Tue, 02 Aug 2022 14:17:12: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:17:12: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:17:30: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:17:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206511/SRX15206511.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:17:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206511/SRX15206511.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:17:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206511/SRX15206511.20_summits.bed INFO @ Tue, 02 Aug 2022 14:17:39: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (503 records, 4 fields): 21 millis CompletedMACS2peakCalling BigWig に変換しました。