Job ID = 14167258 SRX = SRX7848958 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 47501762 spots for SRR11237238/SRR11237238.sra Written 47501762 spots for SRR11237238/SRR11237238.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167913 ("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: 00:17:19 47501762 reads; of these: 47501762 (100.00%) were unpaired; of these: 2270774 (4.78%) aligned 0 times 31786601 (66.92%) aligned exactly 1 time 13444387 (28.30%) aligned >1 times 95.22% overall alignment rate Time searching: 00:17:19 Overall time: 00:17:19 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 20 files... [bam_rmdupse_core] 16369226 / 45230988 = 0.3619 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 11:48:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7848958/SRX7848958.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7848958/SRX7848958.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7848958/SRX7848958.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7848958/SRX7848958.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 11:48:07: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:48:07: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:48:12: 1000000 INFO @ Fri, 10 Dec 2021 11:48:17: 2000000 INFO @ Fri, 10 Dec 2021 11:48:21: 3000000 INFO @ Fri, 10 Dec 2021 11:48:26: 4000000 INFO @ Fri, 10 Dec 2021 11:48:31: 5000000 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 11:48:36: 6000000 INFO @ Fri, 10 Dec 2021 11:48:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7848958/SRX7848958.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7848958/SRX7848958.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7848958/SRX7848958.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7848958/SRX7848958.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 11:48:37: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:48:37: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:48:41: 7000000 INFO @ Fri, 10 Dec 2021 11:48:42: 1000000 INFO @ Fri, 10 Dec 2021 11:48:46: 8000000 INFO @ Fri, 10 Dec 2021 11:48:47: 2000000 INFO @ Fri, 10 Dec 2021 11:48:51: 9000000 INFO @ Fri, 10 Dec 2021 11:48:52: 3000000 INFO @ Fri, 10 Dec 2021 11:48:57: 10000000 INFO @ Fri, 10 Dec 2021 11:48:58: 4000000 INFO @ Fri, 10 Dec 2021 11:49:02: 11000000 INFO @ Fri, 10 Dec 2021 11:49:03: 5000000 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 11:49:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7848958/SRX7848958.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7848958/SRX7848958.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7848958/SRX7848958.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7848958/SRX7848958.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 11:49:07: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:49:07: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:49:07: 12000000 INFO @ Fri, 10 Dec 2021 11:49:08: 6000000 INFO @ Fri, 10 Dec 2021 11:49:12: 1000000 INFO @ Fri, 10 Dec 2021 11:49:12: 13000000 INFO @ Fri, 10 Dec 2021 11:49:14: 7000000 INFO @ Fri, 10 Dec 2021 11:49:18: 2000000 INFO @ Fri, 10 Dec 2021 11:49:18: 14000000 INFO @ Fri, 10 Dec 2021 11:49:19: 8000000 INFO @ Fri, 10 Dec 2021 11:49:23: 15000000 INFO @ Fri, 10 Dec 2021 11:49:23: 3000000 INFO @ Fri, 10 Dec 2021 11:49:25: 9000000 INFO @ Fri, 10 Dec 2021 11:49:28: 16000000 INFO @ Fri, 10 Dec 2021 11:49:29: 4000000 INFO @ Fri, 10 Dec 2021 11:49:30: 10000000 INFO @ Fri, 10 Dec 2021 11:49:34: 17000000 INFO @ Fri, 10 Dec 2021 11:49:34: 5000000 INFO @ Fri, 10 Dec 2021 11:49:36: 11000000 INFO @ Fri, 10 Dec 2021 11:49:39: 18000000 INFO @ Fri, 10 Dec 2021 11:49:40: 6000000 INFO @ Fri, 10 Dec 2021 11:49:41: 12000000 INFO @ Fri, 10 Dec 2021 11:49:44: 19000000 INFO @ Fri, 10 Dec 2021 11:49:45: 7000000 INFO @ Fri, 10 Dec 2021 11:49:46: 13000000 INFO @ Fri, 10 Dec 2021 11:49:50: 20000000 INFO @ Fri, 10 Dec 2021 11:49:51: 8000000 INFO @ Fri, 10 Dec 2021 11:49:52: 14000000 INFO @ Fri, 10 Dec 2021 11:49:55: 21000000 INFO @ Fri, 10 Dec 2021 11:49:56: 9000000 INFO @ Fri, 10 Dec 2021 11:49:58: 15000000 INFO @ Fri, 10 Dec 2021 11:50:00: 22000000 INFO @ Fri, 10 Dec 2021 11:50:02: 10000000 INFO @ Fri, 10 Dec 2021 11:50:03: 16000000 INFO @ Fri, 10 Dec 2021 11:50:06: 23000000 INFO @ Fri, 10 Dec 2021 11:50:07: 11000000 INFO @ Fri, 10 Dec 2021 11:50:08: 17000000 INFO @ Fri, 10 Dec 2021 11:50:11: 24000000 INFO @ Fri, 10 Dec 2021 11:50:13: 12000000 INFO @ Fri, 10 Dec 2021 11:50:14: 18000000 INFO @ Fri, 10 Dec 2021 11:50:16: 25000000 INFO @ Fri, 10 Dec 2021 11:50:18: 13000000 INFO @ Fri, 10 Dec 2021 11:50:19: 19000000 INFO @ Fri, 10 Dec 2021 11:50:21: 26000000 INFO @ Fri, 10 Dec 2021 11:50:23: 14000000 INFO @ Fri, 10 Dec 2021 11:50:25: 20000000 INFO @ Fri, 10 Dec 2021 11:50:27: 27000000 INFO @ Fri, 10 Dec 2021 11:50:29: 15000000 INFO @ Fri, 10 Dec 2021 11:50:30: 21000000 INFO @ Fri, 10 Dec 2021 11:50:32: 28000000 INFO @ Fri, 10 Dec 2021 11:50:34: 16000000 INFO @ Fri, 10 Dec 2021 11:50:36: 22000000 INFO @ Fri, 10 Dec 2021 11:50:37: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 11:50:37: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 11:50:37: #1 total tags in treatment: 28861762 INFO @ Fri, 10 Dec 2021 11:50:37: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:50:37: #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 11:50:37: #1 tags after filtering in treatment: 28861762 INFO @ Fri, 10 Dec 2021 11:50:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:50:37: #1 finished! INFO @ Fri, 10 Dec 2021 11:50:37: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:50:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:50:39: #2 number of paired peaks: 542 WARNING @ Fri, 10 Dec 2021 11:50:39: Fewer paired peaks (542) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 542 pairs to build model! INFO @ Fri, 10 Dec 2021 11:50:39: start model_add_line... INFO @ Fri, 10 Dec 2021 11:50:39: start X-correlation... INFO @ Fri, 10 Dec 2021 11:50:39: end of X-cor INFO @ Fri, 10 Dec 2021 11:50:39: #2 finished! INFO @ Fri, 10 Dec 2021 11:50:39: #2 predicted fragment length is 185 bps INFO @ Fri, 10 Dec 2021 11:50:39: #2 alternative fragment length(s) may be 185 bps INFO @ Fri, 10 Dec 2021 11:50:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7848958/SRX7848958.05_model.r INFO @ Fri, 10 Dec 2021 11:50:39: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:50:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:50:40: 17000000 INFO @ Fri, 10 Dec 2021 11:50:41: 23000000 INFO @ Fri, 10 Dec 2021 11:50:45: 18000000 INFO @ Fri, 10 Dec 2021 11:50:46: 24000000 INFO @ Fri, 10 Dec 2021 11:50:50: 19000000 INFO @ Fri, 10 Dec 2021 11:50:52: 25000000 INFO @ Fri, 10 Dec 2021 11:50:55: 20000000 INFO @ Fri, 10 Dec 2021 11:50:57: 26000000 INFO @ Fri, 10 Dec 2021 11:51:01: 21000000 INFO @ Fri, 10 Dec 2021 11:51:02: 27000000 INFO @ Fri, 10 Dec 2021 11:51:06: 22000000 INFO @ Fri, 10 Dec 2021 11:51:07: 28000000 INFO @ Fri, 10 Dec 2021 11:51:11: 23000000 INFO @ Fri, 10 Dec 2021 11:51:12: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 11:51:12: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 11:51:12: #1 total tags in treatment: 28861762 INFO @ Fri, 10 Dec 2021 11:51:12: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:51:12: #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 11:51:12: #1 tags after filtering in treatment: 28861762 INFO @ Fri, 10 Dec 2021 11:51:12: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:51:12: #1 finished! INFO @ Fri, 10 Dec 2021 11:51:12: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:51:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:51:14: #2 number of paired peaks: 542 WARNING @ Fri, 10 Dec 2021 11:51:14: Fewer paired peaks (542) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 542 pairs to build model! INFO @ Fri, 10 Dec 2021 11:51:14: start model_add_line... INFO @ Fri, 10 Dec 2021 11:51:15: start X-correlation... INFO @ Fri, 10 Dec 2021 11:51:15: end of X-cor INFO @ Fri, 10 Dec 2021 11:51:15: #2 finished! INFO @ Fri, 10 Dec 2021 11:51:15: #2 predicted fragment length is 185 bps INFO @ Fri, 10 Dec 2021 11:51:15: #2 alternative fragment length(s) may be 185 bps INFO @ Fri, 10 Dec 2021 11:51:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7848958/SRX7848958.10_model.r INFO @ Fri, 10 Dec 2021 11:51:15: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:51:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:51:16: 24000000 INFO @ Fri, 10 Dec 2021 11:51:21: 25000000 INFO @ Fri, 10 Dec 2021 11:51:26: 26000000 INFO @ Fri, 10 Dec 2021 11:51:31: 27000000 INFO @ Fri, 10 Dec 2021 11:51:36: 28000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 11:51:41: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 11:51:41: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 11:51:41: #1 total tags in treatment: 28861762 INFO @ Fri, 10 Dec 2021 11:51:41: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:51:41: #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 11:51:41: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:51:41: #1 tags after filtering in treatment: 28861762 INFO @ Fri, 10 Dec 2021 11:51:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:51:41: #1 finished! INFO @ Fri, 10 Dec 2021 11:51:41: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:51:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:51:43: #2 number of paired peaks: 542 WARNING @ Fri, 10 Dec 2021 11:51:43: Fewer paired peaks (542) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 542 pairs to build model! INFO @ Fri, 10 Dec 2021 11:51:43: start model_add_line... INFO @ Fri, 10 Dec 2021 11:51:43: start X-correlation... INFO @ Fri, 10 Dec 2021 11:51:43: end of X-cor INFO @ Fri, 10 Dec 2021 11:51:43: #2 finished! INFO @ Fri, 10 Dec 2021 11:51:43: #2 predicted fragment length is 185 bps INFO @ Fri, 10 Dec 2021 11:51:43: #2 alternative fragment length(s) may be 185 bps INFO @ Fri, 10 Dec 2021 11:51:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7848958/SRX7848958.20_model.r INFO @ Fri, 10 Dec 2021 11:51:44: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:51:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:52:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7848958/SRX7848958.05_peaks.xls INFO @ Fri, 10 Dec 2021 11:52:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7848958/SRX7848958.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:52:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7848958/SRX7848958.05_summits.bed INFO @ Fri, 10 Dec 2021 11:52:08: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (8279 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:52:16: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:52:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7848958/SRX7848958.10_peaks.xls INFO @ Fri, 10 Dec 2021 11:52:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7848958/SRX7848958.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:52:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7848958/SRX7848958.10_summits.bed INFO @ Fri, 10 Dec 2021 11:52:43: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6060 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:52:44: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 11:53:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7848958/SRX7848958.20_peaks.xls INFO @ Fri, 10 Dec 2021 11:53:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7848958/SRX7848958.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:53:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7848958/SRX7848958.20_summits.bed INFO @ Fri, 10 Dec 2021 11:53:10: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3873 records, 4 fields): 6 millis CompletedMACS2peakCalling