Job ID = 14170367 SRX = SRX9720902 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 27358813 spots for SRR13291892/SRR13291892.sra Written 27358813 spots for SRR13291892/SRR13291892.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170772 ("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: 00:10:11 27358813 reads; of these: 27358813 (100.00%) were unpaired; of these: 1214659 (4.44%) aligned 0 times 17921184 (65.50%) aligned exactly 1 time 8222970 (30.06%) aligned >1 times 95.56% overall alignment rate Time searching: 00:10:11 Overall time: 00:10:11 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] 5217662 / 26144154 = 0.1996 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 @ Sat, 11 Dec 2021 06:38:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720902/SRX9720902.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720902/SRX9720902.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720902/SRX9720902.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720902/SRX9720902.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 @ Sat, 11 Dec 2021 06:38:32: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:38:32: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:38:38: 1000000 INFO @ Sat, 11 Dec 2021 06:38:44: 2000000 INFO @ Sat, 11 Dec 2021 06:38:49: 3000000 INFO @ Sat, 11 Dec 2021 06:38:55: 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 @ Sat, 11 Dec 2021 06:39:00: 5000000 INFO @ Sat, 11 Dec 2021 06:39:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720902/SRX9720902.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720902/SRX9720902.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720902/SRX9720902.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720902/SRX9720902.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 @ Sat, 11 Dec 2021 06:39:02: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:39:02: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:39:06: 6000000 INFO @ Sat, 11 Dec 2021 06:39:07: 1000000 INFO @ Sat, 11 Dec 2021 06:39:12: 7000000 INFO @ Sat, 11 Dec 2021 06:39:12: 2000000 INFO @ Sat, 11 Dec 2021 06:39:17: 8000000 INFO @ Sat, 11 Dec 2021 06:39:17: 3000000 INFO @ Sat, 11 Dec 2021 06:39:23: 4000000 INFO @ Sat, 11 Dec 2021 06:39:23: 9000000 INFO @ Sat, 11 Dec 2021 06:39:28: 5000000 INFO @ Sat, 11 Dec 2021 06:39:29: 10000000 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 @ Sat, 11 Dec 2021 06:39:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720902/SRX9720902.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720902/SRX9720902.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720902/SRX9720902.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720902/SRX9720902.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 @ Sat, 11 Dec 2021 06:39:32: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:39:32: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:39:33: 6000000 INFO @ Sat, 11 Dec 2021 06:39:35: 11000000 INFO @ Sat, 11 Dec 2021 06:39:37: 1000000 INFO @ Sat, 11 Dec 2021 06:39:38: 7000000 INFO @ Sat, 11 Dec 2021 06:39:40: 12000000 INFO @ Sat, 11 Dec 2021 06:39:42: 2000000 INFO @ Sat, 11 Dec 2021 06:39:43: 8000000 INFO @ Sat, 11 Dec 2021 06:39:46: 13000000 INFO @ Sat, 11 Dec 2021 06:39:48: 3000000 INFO @ Sat, 11 Dec 2021 06:39:49: 9000000 INFO @ Sat, 11 Dec 2021 06:39:52: 14000000 INFO @ Sat, 11 Dec 2021 06:39:53: 4000000 INFO @ Sat, 11 Dec 2021 06:39:54: 10000000 INFO @ Sat, 11 Dec 2021 06:39:58: 5000000 INFO @ Sat, 11 Dec 2021 06:39:58: 15000000 INFO @ Sat, 11 Dec 2021 06:39:59: 11000000 INFO @ Sat, 11 Dec 2021 06:40:03: 6000000 INFO @ Sat, 11 Dec 2021 06:40:04: 16000000 INFO @ Sat, 11 Dec 2021 06:40:04: 12000000 INFO @ Sat, 11 Dec 2021 06:40:09: 7000000 INFO @ Sat, 11 Dec 2021 06:40:10: 13000000 INFO @ Sat, 11 Dec 2021 06:40:10: 17000000 INFO @ Sat, 11 Dec 2021 06:40:14: 8000000 INFO @ Sat, 11 Dec 2021 06:40:15: 14000000 INFO @ Sat, 11 Dec 2021 06:40:16: 18000000 INFO @ Sat, 11 Dec 2021 06:40:19: 9000000 INFO @ Sat, 11 Dec 2021 06:40:20: 15000000 INFO @ Sat, 11 Dec 2021 06:40:21: 19000000 INFO @ Sat, 11 Dec 2021 06:40:24: 10000000 INFO @ Sat, 11 Dec 2021 06:40:26: 16000000 INFO @ Sat, 11 Dec 2021 06:40:27: 20000000 INFO @ Sat, 11 Dec 2021 06:40:29: 11000000 INFO @ Sat, 11 Dec 2021 06:40:31: 17000000 INFO @ Sat, 11 Dec 2021 06:40:33: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:40:33: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:40:33: #1 total tags in treatment: 20926492 INFO @ Sat, 11 Dec 2021 06:40:33: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:40:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 06:40:33: #1 tags after filtering in treatment: 20926492 INFO @ Sat, 11 Dec 2021 06:40:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:40:33: #1 finished! INFO @ Sat, 11 Dec 2021 06:40:33: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:40:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:40:34: #2 number of paired peaks: 471 WARNING @ Sat, 11 Dec 2021 06:40:34: Fewer paired peaks (471) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 471 pairs to build model! INFO @ Sat, 11 Dec 2021 06:40:34: start model_add_line... INFO @ Sat, 11 Dec 2021 06:40:34: start X-correlation... INFO @ Sat, 11 Dec 2021 06:40:34: end of X-cor INFO @ Sat, 11 Dec 2021 06:40:34: #2 finished! INFO @ Sat, 11 Dec 2021 06:40:34: #2 predicted fragment length is 102 bps INFO @ Sat, 11 Dec 2021 06:40:34: #2 alternative fragment length(s) may be 102 bps INFO @ Sat, 11 Dec 2021 06:40:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720902/SRX9720902.05_model.r INFO @ Sat, 11 Dec 2021 06:40:34: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:40:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:40:35: 12000000 INFO @ Sat, 11 Dec 2021 06:40:36: 18000000 INFO @ Sat, 11 Dec 2021 06:40:40: 13000000 INFO @ Sat, 11 Dec 2021 06:40:41: 19000000 INFO @ Sat, 11 Dec 2021 06:40:45: 14000000 INFO @ Sat, 11 Dec 2021 06:40:46: 20000000 INFO @ Sat, 11 Dec 2021 06:40:50: 15000000 INFO @ Sat, 11 Dec 2021 06:40:51: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:40:51: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:40:51: #1 total tags in treatment: 20926492 INFO @ Sat, 11 Dec 2021 06:40:51: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:40:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 06:40:51: #1 tags after filtering in treatment: 20926492 INFO @ Sat, 11 Dec 2021 06:40:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:40:51: #1 finished! INFO @ Sat, 11 Dec 2021 06:40:51: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:40:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:40:53: #2 number of paired peaks: 471 WARNING @ Sat, 11 Dec 2021 06:40:53: Fewer paired peaks (471) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 471 pairs to build model! INFO @ Sat, 11 Dec 2021 06:40:53: start model_add_line... INFO @ Sat, 11 Dec 2021 06:40:53: start X-correlation... INFO @ Sat, 11 Dec 2021 06:40:53: end of X-cor INFO @ Sat, 11 Dec 2021 06:40:53: #2 finished! INFO @ Sat, 11 Dec 2021 06:40:53: #2 predicted fragment length is 102 bps INFO @ Sat, 11 Dec 2021 06:40:53: #2 alternative fragment length(s) may be 102 bps INFO @ Sat, 11 Dec 2021 06:40:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720902/SRX9720902.10_model.r INFO @ Sat, 11 Dec 2021 06:40:53: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:40:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:40:55: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 06:41:00: 17000000 INFO @ Sat, 11 Dec 2021 06:41:05: 18000000 INFO @ Sat, 11 Dec 2021 06:41:10: 19000000 INFO @ Sat, 11 Dec 2021 06:41:14: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:41:14: 20000000 INFO @ Sat, 11 Dec 2021 06:41:19: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:41:19: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:41:19: #1 total tags in treatment: 20926492 INFO @ Sat, 11 Dec 2021 06:41:19: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:41:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 06:41:19: #1 tags after filtering in treatment: 20926492 INFO @ Sat, 11 Dec 2021 06:41:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:41:19: #1 finished! INFO @ Sat, 11 Dec 2021 06:41:19: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:41:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:41:21: #2 number of paired peaks: 471 WARNING @ Sat, 11 Dec 2021 06:41:21: Fewer paired peaks (471) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 471 pairs to build model! INFO @ Sat, 11 Dec 2021 06:41:21: start model_add_line... INFO @ Sat, 11 Dec 2021 06:41:21: start X-correlation... INFO @ Sat, 11 Dec 2021 06:41:21: end of X-cor INFO @ Sat, 11 Dec 2021 06:41:21: #2 finished! INFO @ Sat, 11 Dec 2021 06:41:21: #2 predicted fragment length is 102 bps INFO @ Sat, 11 Dec 2021 06:41:21: #2 alternative fragment length(s) may be 102 bps INFO @ Sat, 11 Dec 2021 06:41:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720902/SRX9720902.20_model.r INFO @ Sat, 11 Dec 2021 06:41:21: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:41:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:41:31: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:41:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720902/SRX9720902.05_peaks.xls INFO @ Sat, 11 Dec 2021 06:41:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720902/SRX9720902.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:41:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720902/SRX9720902.05_summits.bed INFO @ Sat, 11 Dec 2021 06:41:33: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5510 records, 4 fields): 7 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 06:41:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720902/SRX9720902.10_peaks.xls INFO @ Sat, 11 Dec 2021 06:41:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720902/SRX9720902.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:41:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720902/SRX9720902.10_summits.bed INFO @ Sat, 11 Dec 2021 06:41:49: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3789 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:41:59: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:42:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720902/SRX9720902.20_peaks.xls INFO @ Sat, 11 Dec 2021 06:42:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720902/SRX9720902.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:42:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720902/SRX9720902.20_summits.bed INFO @ Sat, 11 Dec 2021 06:42:18: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2369 records, 4 fields): 3 millis CompletedMACS2peakCalling