Job ID = 16439303 SRX = SRX15206485 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:51:20 prefetch.2.10.7: 1) Downloading 'SRR19139318'... 2022-08-02T05:51:20 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:51:46 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:51:47 prefetch.2.10.7: 'SRR19139318' is valid 2022-08-02T05:51:47 prefetch.2.10.7: 1) 'SRR19139318' was downloaded successfully 2022-08-02T05:51:47 prefetch.2.10.7: 'SRR19139318' has 0 unresolved dependencies Read 22066348 spots for SRR19139318/SRR19139318.sra Written 22066348 spots for SRR19139318/SRR19139318.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439402 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:08:35 22066348 reads; of these: 22066348 (100.00%) were unpaired; of these: 685989 (3.11%) aligned 0 times 17922149 (81.22%) aligned exactly 1 time 3458210 (15.67%) aligned >1 times 96.89% overall alignment rate Time searching: 00:08:36 Overall time: 00:08:36 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] 1540016 / 21380359 = 0.0720 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 15:08:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206485/SRX15206485.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206485/SRX15206485.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206485/SRX15206485.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206485/SRX15206485.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 15:08:04: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:08:04: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:08:13: 1000000 INFO @ Tue, 02 Aug 2022 15:08:21: 2000000 INFO @ Tue, 02 Aug 2022 15:08:30: 3000000 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 15:08:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206485/SRX15206485.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206485/SRX15206485.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206485/SRX15206485.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206485/SRX15206485.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 15:08:33: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:08:33: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:08:39: 4000000 INFO @ Tue, 02 Aug 2022 15:08:45: 1000000 INFO @ Tue, 02 Aug 2022 15:08:49: 5000000 INFO @ Tue, 02 Aug 2022 15:08:56: 2000000 INFO @ Tue, 02 Aug 2022 15:08:59: 6000000 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 15:09:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206485/SRX15206485.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206485/SRX15206485.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206485/SRX15206485.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206485/SRX15206485.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 15:09:03: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:09:03: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:09:05: 3000000 INFO @ Tue, 02 Aug 2022 15:09:07: 7000000 INFO @ Tue, 02 Aug 2022 15:09:14: 1000000 INFO @ Tue, 02 Aug 2022 15:09:14: 4000000 INFO @ Tue, 02 Aug 2022 15:09:16: 8000000 INFO @ Tue, 02 Aug 2022 15:09:24: 9000000 INFO @ Tue, 02 Aug 2022 15:09:25: 5000000 INFO @ Tue, 02 Aug 2022 15:09:25: 2000000 INFO @ Tue, 02 Aug 2022 15:09:33: 10000000 INFO @ Tue, 02 Aug 2022 15:09:35: 6000000 INFO @ Tue, 02 Aug 2022 15:09:35: 3000000 INFO @ Tue, 02 Aug 2022 15:09:41: 11000000 INFO @ Tue, 02 Aug 2022 15:09:45: 4000000 INFO @ Tue, 02 Aug 2022 15:09:45: 7000000 INFO @ Tue, 02 Aug 2022 15:09:50: 12000000 INFO @ Tue, 02 Aug 2022 15:09:55: 8000000 INFO @ Tue, 02 Aug 2022 15:09:56: 5000000 INFO @ Tue, 02 Aug 2022 15:09:59: 13000000 INFO @ Tue, 02 Aug 2022 15:10:04: 9000000 INFO @ Tue, 02 Aug 2022 15:10:07: 6000000 INFO @ Tue, 02 Aug 2022 15:10:08: 14000000 INFO @ Tue, 02 Aug 2022 15:10:14: 10000000 INFO @ Tue, 02 Aug 2022 15:10:16: 15000000 INFO @ Tue, 02 Aug 2022 15:10:18: 7000000 INFO @ Tue, 02 Aug 2022 15:10:23: 11000000 INFO @ Tue, 02 Aug 2022 15:10:25: 16000000 INFO @ Tue, 02 Aug 2022 15:10:29: 8000000 INFO @ Tue, 02 Aug 2022 15:10:33: 12000000 INFO @ Tue, 02 Aug 2022 15:10:34: 17000000 INFO @ Tue, 02 Aug 2022 15:10:40: 9000000 INFO @ Tue, 02 Aug 2022 15:10:42: 18000000 INFO @ Tue, 02 Aug 2022 15:10:43: 13000000 INFO @ Tue, 02 Aug 2022 15:10:51: 10000000 INFO @ Tue, 02 Aug 2022 15:10:51: 19000000 INFO @ Tue, 02 Aug 2022 15:10:53: 14000000 INFO @ Tue, 02 Aug 2022 15:10:59: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 15:10:59: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 15:10:59: #1 total tags in treatment: 19840343 INFO @ Tue, 02 Aug 2022 15:10:59: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:10:59: #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 15:10:59: #1 tags after filtering in treatment: 19840343 INFO @ Tue, 02 Aug 2022 15:10:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:10:59: #1 finished! INFO @ Tue, 02 Aug 2022 15:10:59: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:10:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:11:01: #2 number of paired peaks: 118 WARNING @ Tue, 02 Aug 2022 15:11:01: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Tue, 02 Aug 2022 15:11:01: start model_add_line... INFO @ Tue, 02 Aug 2022 15:11:01: start X-correlation... INFO @ Tue, 02 Aug 2022 15:11:01: end of X-cor INFO @ Tue, 02 Aug 2022 15:11:01: #2 finished! INFO @ Tue, 02 Aug 2022 15:11:01: #2 predicted fragment length is 203 bps INFO @ Tue, 02 Aug 2022 15:11:01: #2 alternative fragment length(s) may be 0,57,109,149,164,203,353,470,551,562,583 bps INFO @ Tue, 02 Aug 2022 15:11:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206485/SRX15206485.05_model.r INFO @ Tue, 02 Aug 2022 15:11:01: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:11:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:11:02: 11000000 INFO @ Tue, 02 Aug 2022 15:11:03: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:11:13: 16000000 INFO @ Tue, 02 Aug 2022 15:11:13: 12000000 INFO @ Tue, 02 Aug 2022 15:11:22: 17000000 INFO @ Tue, 02 Aug 2022 15:11:24: 13000000 INFO @ Tue, 02 Aug 2022 15:11:32: 18000000 INFO @ Tue, 02 Aug 2022 15:11:34: 14000000 INFO @ Tue, 02 Aug 2022 15:11:43: 19000000 INFO @ Tue, 02 Aug 2022 15:11:45: 15000000 INFO @ Tue, 02 Aug 2022 15:11:52: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 15:11:52: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 15:11:52: #1 total tags in treatment: 19840343 INFO @ Tue, 02 Aug 2022 15:11:52: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:11:52: #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 15:11:52: #1 tags after filtering in treatment: 19840343 INFO @ Tue, 02 Aug 2022 15:11:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:11:52: #1 finished! INFO @ Tue, 02 Aug 2022 15:11:52: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:11:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:11:52: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:11:54: #2 number of paired peaks: 118 WARNING @ Tue, 02 Aug 2022 15:11:54: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Tue, 02 Aug 2022 15:11:54: start model_add_line... INFO @ Tue, 02 Aug 2022 15:11:54: start X-correlation... INFO @ Tue, 02 Aug 2022 15:11:54: end of X-cor INFO @ Tue, 02 Aug 2022 15:11:54: #2 finished! INFO @ Tue, 02 Aug 2022 15:11:54: #2 predicted fragment length is 203 bps INFO @ Tue, 02 Aug 2022 15:11:54: #2 alternative fragment length(s) may be 0,57,109,149,164,203,353,470,551,562,583 bps INFO @ Tue, 02 Aug 2022 15:11:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206485/SRX15206485.10_model.r INFO @ Tue, 02 Aug 2022 15:11:54: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:11:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:11:56: 16000000 INFO @ Tue, 02 Aug 2022 15:12:06: 17000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:12:17: 18000000 INFO @ Tue, 02 Aug 2022 15:12:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206485/SRX15206485.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:12:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206485/SRX15206485.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:12:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206485/SRX15206485.05_summits.bed INFO @ Tue, 02 Aug 2022 15:12:19: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (163 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:12:28: 19000000 INFO @ Tue, 02 Aug 2022 15:12:37: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 15:12:37: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 15:12:37: #1 total tags in treatment: 19840343 INFO @ Tue, 02 Aug 2022 15:12:37: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:12:37: #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 15:12:37: #1 tags after filtering in treatment: 19840343 INFO @ Tue, 02 Aug 2022 15:12:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:12:37: #1 finished! INFO @ Tue, 02 Aug 2022 15:12:37: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:12:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:12:39: #2 number of paired peaks: 118 WARNING @ Tue, 02 Aug 2022 15:12:39: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Tue, 02 Aug 2022 15:12:39: start model_add_line... INFO @ Tue, 02 Aug 2022 15:12:39: start X-correlation... INFO @ Tue, 02 Aug 2022 15:12:39: end of X-cor INFO @ Tue, 02 Aug 2022 15:12:39: #2 finished! INFO @ Tue, 02 Aug 2022 15:12:39: #2 predicted fragment length is 203 bps INFO @ Tue, 02 Aug 2022 15:12:39: #2 alternative fragment length(s) may be 0,57,109,149,164,203,353,470,551,562,583 bps INFO @ Tue, 02 Aug 2022 15:12:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206485/SRX15206485.20_model.r INFO @ Tue, 02 Aug 2022 15:12:39: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:12:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:12:47: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:13:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206485/SRX15206485.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:13:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206485/SRX15206485.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:13:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206485/SRX15206485.10_summits.bed INFO @ Tue, 02 Aug 2022 15:13:14: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (78 records, 4 fields): 39 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:13:32: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:14:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206485/SRX15206485.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:14:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206485/SRX15206485.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:14:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206485/SRX15206485.20_summits.bed INFO @ Tue, 02 Aug 2022 15:14:00: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (38 records, 4 fields): 11 millis CompletedMACS2peakCalling