Job ID = 14167032 SRX = SRX8574267 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 33250076 spots for SRR12045588/SRR12045588.sra Written 33250076 spots for SRR12045588/SRR12045588.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167403 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:12:04 33250076 reads; of these: 33250076 (100.00%) were unpaired; of these: 4237387 (12.74%) aligned 0 times 20351963 (61.21%) aligned exactly 1 time 8660726 (26.05%) aligned >1 times 87.26% overall alignment rate Time searching: 00:12:05 Overall time: 00:12:05 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] 7102118 / 29012689 = 0.2448 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 09:21:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8574267/SRX8574267.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8574267/SRX8574267.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8574267/SRX8574267.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8574267/SRX8574267.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 @ Fri, 10 Dec 2021 09:21:17: #1 read tag files... INFO @ Fri, 10 Dec 2021 09:21:17: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 09:21:24: 1000000 INFO @ Fri, 10 Dec 2021 09:21:29: 2000000 INFO @ Fri, 10 Dec 2021 09:21:35: 3000000 INFO @ Fri, 10 Dec 2021 09:21:42: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 09:21:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8574267/SRX8574267.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8574267/SRX8574267.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8574267/SRX8574267.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8574267/SRX8574267.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 @ Fri, 10 Dec 2021 09:21:46: #1 read tag files... INFO @ Fri, 10 Dec 2021 09:21:46: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 09:21:48: 5000000 INFO @ Fri, 10 Dec 2021 09:21:54: 1000000 INFO @ Fri, 10 Dec 2021 09:21:55: 6000000 INFO @ Fri, 10 Dec 2021 09:22:01: 7000000 INFO @ Fri, 10 Dec 2021 09:22:02: 2000000 INFO @ Fri, 10 Dec 2021 09:22:09: 8000000 INFO @ Fri, 10 Dec 2021 09:22:11: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 09:22:15: 9000000 INFO @ Fri, 10 Dec 2021 09:22:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8574267/SRX8574267.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8574267/SRX8574267.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8574267/SRX8574267.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8574267/SRX8574267.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 @ Fri, 10 Dec 2021 09:22:15: #1 read tag files... INFO @ Fri, 10 Dec 2021 09:22:15: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 09:22:20: 4000000 INFO @ Fri, 10 Dec 2021 09:22:21: 10000000 INFO @ Fri, 10 Dec 2021 09:22:24: 1000000 INFO @ Fri, 10 Dec 2021 09:22:27: 11000000 INFO @ Fri, 10 Dec 2021 09:22:28: 5000000 INFO @ Fri, 10 Dec 2021 09:22:33: 2000000 INFO @ Fri, 10 Dec 2021 09:22:33: 12000000 INFO @ Fri, 10 Dec 2021 09:22:37: 6000000 INFO @ Fri, 10 Dec 2021 09:22:40: 13000000 INFO @ Fri, 10 Dec 2021 09:22:42: 3000000 INFO @ Fri, 10 Dec 2021 09:22:46: 7000000 INFO @ Fri, 10 Dec 2021 09:22:46: 14000000 INFO @ Fri, 10 Dec 2021 09:22:50: 4000000 INFO @ Fri, 10 Dec 2021 09:22:52: 15000000 INFO @ Fri, 10 Dec 2021 09:22:54: 8000000 INFO @ Fri, 10 Dec 2021 09:22:58: 16000000 INFO @ Fri, 10 Dec 2021 09:22:59: 5000000 INFO @ Fri, 10 Dec 2021 09:23:04: 9000000 INFO @ Fri, 10 Dec 2021 09:23:04: 17000000 INFO @ Fri, 10 Dec 2021 09:23:08: 6000000 INFO @ Fri, 10 Dec 2021 09:23:11: 18000000 INFO @ Fri, 10 Dec 2021 09:23:12: 10000000 INFO @ Fri, 10 Dec 2021 09:23:17: 7000000 INFO @ Fri, 10 Dec 2021 09:23:17: 19000000 INFO @ Fri, 10 Dec 2021 09:23:21: 11000000 INFO @ Fri, 10 Dec 2021 09:23:23: 20000000 INFO @ Fri, 10 Dec 2021 09:23:26: 8000000 INFO @ Fri, 10 Dec 2021 09:23:30: 12000000 INFO @ Fri, 10 Dec 2021 09:23:30: 21000000 INFO @ Fri, 10 Dec 2021 09:23:35: 9000000 INFO @ Fri, 10 Dec 2021 09:23:36: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 09:23:36: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 09:23:36: #1 total tags in treatment: 21910571 INFO @ Fri, 10 Dec 2021 09:23:36: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 09:23:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 09:23:36: #1 tags after filtering in treatment: 21910571 INFO @ Fri, 10 Dec 2021 09:23:36: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 09:23:36: #1 finished! INFO @ Fri, 10 Dec 2021 09:23:36: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 09:23:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 09:23:38: #2 number of paired peaks: 886 WARNING @ Fri, 10 Dec 2021 09:23:38: Fewer paired peaks (886) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 886 pairs to build model! INFO @ Fri, 10 Dec 2021 09:23:38: start model_add_line... INFO @ Fri, 10 Dec 2021 09:23:38: start X-correlation... INFO @ Fri, 10 Dec 2021 09:23:38: end of X-cor INFO @ Fri, 10 Dec 2021 09:23:38: #2 finished! INFO @ Fri, 10 Dec 2021 09:23:38: #2 predicted fragment length is 232 bps INFO @ Fri, 10 Dec 2021 09:23:38: #2 alternative fragment length(s) may be 232 bps INFO @ Fri, 10 Dec 2021 09:23:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8574267/SRX8574267.05_model.r INFO @ Fri, 10 Dec 2021 09:23:38: #3 Call peaks... INFO @ Fri, 10 Dec 2021 09:23:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 09:23:38: 13000000 INFO @ Fri, 10 Dec 2021 09:23:44: 10000000 INFO @ Fri, 10 Dec 2021 09:23:47: 14000000 INFO @ Fri, 10 Dec 2021 09:23:53: 11000000 INFO @ Fri, 10 Dec 2021 09:23:56: 15000000 INFO @ Fri, 10 Dec 2021 09:24:02: 12000000 INFO @ Fri, 10 Dec 2021 09:24:05: 16000000 INFO @ Fri, 10 Dec 2021 09:24:11: 13000000 INFO @ Fri, 10 Dec 2021 09:24:13: 17000000 INFO @ Fri, 10 Dec 2021 09:24:19: 14000000 INFO @ Fri, 10 Dec 2021 09:24:22: 18000000 INFO @ Fri, 10 Dec 2021 09:24:24: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 09:24:28: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 09:24:31: 19000000 INFO @ Fri, 10 Dec 2021 09:24:37: 16000000 INFO @ Fri, 10 Dec 2021 09:24:40: 20000000 INFO @ Fri, 10 Dec 2021 09:24:46: 17000000 INFO @ Fri, 10 Dec 2021 09:24:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8574267/SRX8574267.05_peaks.xls INFO @ Fri, 10 Dec 2021 09:24:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8574267/SRX8574267.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 09:24:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8574267/SRX8574267.05_summits.bed INFO @ Fri, 10 Dec 2021 09:24:47: Done! INFO @ Fri, 10 Dec 2021 09:24:48: 21000000 pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (5854 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 09:24:55: 18000000 INFO @ Fri, 10 Dec 2021 09:24:56: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 09:24:56: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 09:24:56: #1 total tags in treatment: 21910571 INFO @ Fri, 10 Dec 2021 09:24:56: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 09:24:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 09:24:56: #1 tags after filtering in treatment: 21910571 INFO @ Fri, 10 Dec 2021 09:24:56: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 09:24:56: #1 finished! INFO @ Fri, 10 Dec 2021 09:24:56: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 09:24:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 09:24:58: #2 number of paired peaks: 886 WARNING @ Fri, 10 Dec 2021 09:24:58: Fewer paired peaks (886) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 886 pairs to build model! INFO @ Fri, 10 Dec 2021 09:24:58: start model_add_line... INFO @ Fri, 10 Dec 2021 09:24:58: start X-correlation... INFO @ Fri, 10 Dec 2021 09:24:58: end of X-cor INFO @ Fri, 10 Dec 2021 09:24:58: #2 finished! INFO @ Fri, 10 Dec 2021 09:24:58: #2 predicted fragment length is 232 bps INFO @ Fri, 10 Dec 2021 09:24:58: #2 alternative fragment length(s) may be 232 bps INFO @ Fri, 10 Dec 2021 09:24:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8574267/SRX8574267.10_model.r INFO @ Fri, 10 Dec 2021 09:24:58: #3 Call peaks... INFO @ Fri, 10 Dec 2021 09:24:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 09:25:04: 19000000 INFO @ Fri, 10 Dec 2021 09:25:12: 20000000 INFO @ Fri, 10 Dec 2021 09:25:21: 21000000 INFO @ Fri, 10 Dec 2021 09:25:28: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 09:25:28: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 09:25:28: #1 total tags in treatment: 21910571 INFO @ Fri, 10 Dec 2021 09:25:28: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 09:25:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 09:25:29: #1 tags after filtering in treatment: 21910571 INFO @ Fri, 10 Dec 2021 09:25:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 09:25:29: #1 finished! INFO @ Fri, 10 Dec 2021 09:25:29: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 09:25:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 09:25:30: #2 number of paired peaks: 886 WARNING @ Fri, 10 Dec 2021 09:25:30: Fewer paired peaks (886) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 886 pairs to build model! INFO @ Fri, 10 Dec 2021 09:25:30: start model_add_line... INFO @ Fri, 10 Dec 2021 09:25:31: start X-correlation... INFO @ Fri, 10 Dec 2021 09:25:31: end of X-cor INFO @ Fri, 10 Dec 2021 09:25:31: #2 finished! INFO @ Fri, 10 Dec 2021 09:25:31: #2 predicted fragment length is 232 bps INFO @ Fri, 10 Dec 2021 09:25:31: #2 alternative fragment length(s) may be 232 bps INFO @ Fri, 10 Dec 2021 09:25:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8574267/SRX8574267.20_model.r INFO @ Fri, 10 Dec 2021 09:25:31: #3 Call peaks... INFO @ Fri, 10 Dec 2021 09:25:31: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 09:25:45: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 09:26:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8574267/SRX8574267.10_peaks.xls INFO @ Fri, 10 Dec 2021 09:26:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8574267/SRX8574267.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 09:26:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8574267/SRX8574267.10_summits.bed INFO @ Fri, 10 Dec 2021 09:26:08: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4633 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 09:26:18: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 09:26:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8574267/SRX8574267.20_peaks.xls INFO @ Fri, 10 Dec 2021 09:26:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8574267/SRX8574267.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 09:26:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8574267/SRX8574267.20_summits.bed INFO @ Fri, 10 Dec 2021 09:26:41: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3410 records, 4 fields): 6 millis CompletedMACS2peakCalling