Job ID = 16437422 SRX = SRX15046047 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 30902359 spots for SRR18970069/SRR18970069.sra Written 30902359 spots for SRR18970069/SRR18970069.sra fastq に変換しました。 bowtie でマッピング中... Your job 16437480 ("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: 00:08:50 30902359 reads; of these: 30902359 (100.00%) were unpaired; of these: 4323047 (13.99%) aligned 0 times 21846113 (70.69%) aligned exactly 1 time 4733199 (15.32%) aligned >1 times 86.01% overall alignment rate Time searching: 00:08:50 Overall time: 00:08:50 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] 7357988 / 26579312 = 0.2768 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 12:41:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15046047/SRX15046047.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15046047/SRX15046047.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15046047/SRX15046047.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15046047/SRX15046047.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 12:41:55: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:41:55: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:42:03: 1000000 INFO @ Tue, 02 Aug 2022 12:42:10: 2000000 INFO @ Tue, 02 Aug 2022 12:42:18: 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 12:42:25: 4000000 INFO @ Tue, 02 Aug 2022 12:42:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15046047/SRX15046047.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15046047/SRX15046047.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15046047/SRX15046047.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15046047/SRX15046047.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 12:42:25: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:42:25: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:42:33: 1000000 INFO @ Tue, 02 Aug 2022 12:42:33: 5000000 INFO @ Tue, 02 Aug 2022 12:42:41: 2000000 INFO @ Tue, 02 Aug 2022 12:42:41: 6000000 INFO @ Tue, 02 Aug 2022 12:42:49: 3000000 INFO @ Tue, 02 Aug 2022 12:42:49: 7000000 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 12:42:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15046047/SRX15046047.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15046047/SRX15046047.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15046047/SRX15046047.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15046047/SRX15046047.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 12:42:55: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:42:55: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:42:56: 4000000 INFO @ Tue, 02 Aug 2022 12:42:58: 8000000 INFO @ Tue, 02 Aug 2022 12:43:04: 1000000 INFO @ Tue, 02 Aug 2022 12:43:04: 5000000 INFO @ Tue, 02 Aug 2022 12:43:06: 9000000 INFO @ Tue, 02 Aug 2022 12:43:12: 6000000 INFO @ Tue, 02 Aug 2022 12:43:12: 2000000 INFO @ Tue, 02 Aug 2022 12:43:14: 10000000 INFO @ Tue, 02 Aug 2022 12:43:19: 7000000 INFO @ Tue, 02 Aug 2022 12:43:21: 3000000 INFO @ Tue, 02 Aug 2022 12:43:22: 11000000 INFO @ Tue, 02 Aug 2022 12:43:26: 8000000 INFO @ Tue, 02 Aug 2022 12:43:29: 4000000 INFO @ Tue, 02 Aug 2022 12:43:30: 12000000 INFO @ Tue, 02 Aug 2022 12:43:34: 9000000 INFO @ Tue, 02 Aug 2022 12:43:37: 5000000 INFO @ Tue, 02 Aug 2022 12:43:38: 13000000 INFO @ Tue, 02 Aug 2022 12:43:41: 10000000 INFO @ Tue, 02 Aug 2022 12:43:45: 6000000 INFO @ Tue, 02 Aug 2022 12:43:47: 14000000 INFO @ Tue, 02 Aug 2022 12:43:48: 11000000 INFO @ Tue, 02 Aug 2022 12:43:54: 7000000 INFO @ Tue, 02 Aug 2022 12:43:55: 15000000 INFO @ Tue, 02 Aug 2022 12:43:55: 12000000 INFO @ Tue, 02 Aug 2022 12:44:02: 8000000 INFO @ Tue, 02 Aug 2022 12:44:03: 13000000 INFO @ Tue, 02 Aug 2022 12:44:03: 16000000 INFO @ Tue, 02 Aug 2022 12:44:10: 14000000 INFO @ Tue, 02 Aug 2022 12:44:10: 9000000 INFO @ Tue, 02 Aug 2022 12:44:11: 17000000 INFO @ Tue, 02 Aug 2022 12:44:17: 15000000 INFO @ Tue, 02 Aug 2022 12:44:18: 10000000 INFO @ Tue, 02 Aug 2022 12:44:20: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 12:44:25: 16000000 INFO @ Tue, 02 Aug 2022 12:44:27: 11000000 INFO @ Tue, 02 Aug 2022 12:44:28: 19000000 INFO @ Tue, 02 Aug 2022 12:44:29: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 12:44:29: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 12:44:29: #1 total tags in treatment: 19221324 INFO @ Tue, 02 Aug 2022 12:44:29: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:44:29: #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 12:44:30: #1 tags after filtering in treatment: 19221324 INFO @ Tue, 02 Aug 2022 12:44:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 12:44:30: #1 finished! INFO @ Tue, 02 Aug 2022 12:44:30: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:44:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:44:31: #2 number of paired peaks: 157 WARNING @ Tue, 02 Aug 2022 12:44:31: Fewer paired peaks (157) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 157 pairs to build model! INFO @ Tue, 02 Aug 2022 12:44:31: start model_add_line... INFO @ Tue, 02 Aug 2022 12:44:31: start X-correlation... INFO @ Tue, 02 Aug 2022 12:44:31: end of X-cor INFO @ Tue, 02 Aug 2022 12:44:31: #2 finished! INFO @ Tue, 02 Aug 2022 12:44:31: #2 predicted fragment length is 127 bps INFO @ Tue, 02 Aug 2022 12:44:31: #2 alternative fragment length(s) may be 127 bps INFO @ Tue, 02 Aug 2022 12:44:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15046047/SRX15046047.05_model.r INFO @ Tue, 02 Aug 2022 12:44:31: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:44:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:44:32: 17000000 INFO @ Tue, 02 Aug 2022 12:44:34: 12000000 INFO @ Tue, 02 Aug 2022 12:44:39: 18000000 INFO @ Tue, 02 Aug 2022 12:44:42: 13000000 INFO @ Tue, 02 Aug 2022 12:44:46: 19000000 INFO @ Tue, 02 Aug 2022 12:44:48: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 12:44:48: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 12:44:48: #1 total tags in treatment: 19221324 INFO @ Tue, 02 Aug 2022 12:44:48: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:44:48: #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 12:44:48: #1 tags after filtering in treatment: 19221324 INFO @ Tue, 02 Aug 2022 12:44:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 12:44:48: #1 finished! INFO @ Tue, 02 Aug 2022 12:44:48: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:44:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:44:49: #2 number of paired peaks: 157 WARNING @ Tue, 02 Aug 2022 12:44:49: Fewer paired peaks (157) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 157 pairs to build model! INFO @ Tue, 02 Aug 2022 12:44:49: start model_add_line... INFO @ Tue, 02 Aug 2022 12:44:50: start X-correlation... INFO @ Tue, 02 Aug 2022 12:44:50: end of X-cor INFO @ Tue, 02 Aug 2022 12:44:50: #2 finished! INFO @ Tue, 02 Aug 2022 12:44:50: #2 predicted fragment length is 127 bps INFO @ Tue, 02 Aug 2022 12:44:50: #2 alternative fragment length(s) may be 127 bps INFO @ Tue, 02 Aug 2022 12:44:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15046047/SRX15046047.10_model.r INFO @ Tue, 02 Aug 2022 12:44:50: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:44:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:44:50: 14000000 INFO @ Tue, 02 Aug 2022 12:44:57: 15000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 12:45:04: 16000000 INFO @ Tue, 02 Aug 2022 12:45:09: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:45:11: 17000000 INFO @ Tue, 02 Aug 2022 12:45:19: 18000000 INFO @ Tue, 02 Aug 2022 12:45:25: 19000000 INFO @ Tue, 02 Aug 2022 12:45:26: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:45:27: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 12:45:27: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 12:45:27: #1 total tags in treatment: 19221324 INFO @ Tue, 02 Aug 2022 12:45:27: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:45:27: #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 12:45:27: #1 tags after filtering in treatment: 19221324 INFO @ Tue, 02 Aug 2022 12:45:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 12:45:27: #1 finished! INFO @ Tue, 02 Aug 2022 12:45:27: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:45:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:45:28: #2 number of paired peaks: 157 WARNING @ Tue, 02 Aug 2022 12:45:28: Fewer paired peaks (157) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 157 pairs to build model! INFO @ Tue, 02 Aug 2022 12:45:28: start model_add_line... INFO @ Tue, 02 Aug 2022 12:45:29: start X-correlation... INFO @ Tue, 02 Aug 2022 12:45:29: end of X-cor INFO @ Tue, 02 Aug 2022 12:45:29: #2 finished! INFO @ Tue, 02 Aug 2022 12:45:29: #2 predicted fragment length is 127 bps INFO @ Tue, 02 Aug 2022 12:45:29: #2 alternative fragment length(s) may be 127 bps INFO @ Tue, 02 Aug 2022 12:45:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15046047/SRX15046047.20_model.r INFO @ Tue, 02 Aug 2022 12:45:29: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:45:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:45:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15046047/SRX15046047.05_peaks.xls INFO @ Tue, 02 Aug 2022 12:45:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15046047/SRX15046047.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:45:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15046047/SRX15046047.05_summits.bed INFO @ Tue, 02 Aug 2022 12:45:30: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4247 records, 4 fields): 66 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 12:45:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15046047/SRX15046047.10_peaks.xls INFO @ Tue, 02 Aug 2022 12:45:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15046047/SRX15046047.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:45:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15046047/SRX15046047.10_summits.bed INFO @ Tue, 02 Aug 2022 12:45:44: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (2746 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 12:46:06: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:46:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15046047/SRX15046047.20_peaks.xls INFO @ Tue, 02 Aug 2022 12:46:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15046047/SRX15046047.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:46:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15046047/SRX15046047.20_summits.bed INFO @ Tue, 02 Aug 2022 12:46:26: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1627 records, 4 fields): 32 millis CompletedMACS2peakCalling