Job ID = 14170428 SRX = SRX8784757 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 6725335 spots for SRR12280887/SRR12280887.sra Written 6725335 spots for SRR12280887/SRR12280887.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170821 ("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: 00:02:34 6725335 reads; of these: 6725335 (100.00%) were unpaired; of these: 247050 (3.67%) aligned 0 times 6135106 (91.22%) aligned exactly 1 time 343179 (5.10%) aligned >1 times 96.33% overall alignment rate Time searching: 00:02:34 Overall time: 00:02:34 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_rmdupse_core] 340640 / 6478285 = 0.0526 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 06:51:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8784757/SRX8784757.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8784757/SRX8784757.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8784757/SRX8784757.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8784757/SRX8784757.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 06:51:37: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:51:37: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:51:43: 1000000 INFO @ Sat, 11 Dec 2021 06:51:50: 2000000 INFO @ Sat, 11 Dec 2021 06:51:56: 3000000 INFO @ Sat, 11 Dec 2021 06:52:03: 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 06:52:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8784757/SRX8784757.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8784757/SRX8784757.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8784757/SRX8784757.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8784757/SRX8784757.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 06:52:07: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:52:07: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:52:10: 5000000 INFO @ Sat, 11 Dec 2021 06:52:14: 1000000 INFO @ Sat, 11 Dec 2021 06:52:17: 6000000 INFO @ Sat, 11 Dec 2021 06:52:18: #1 tag size is determined as 95 bps INFO @ Sat, 11 Dec 2021 06:52:18: #1 tag size = 95 INFO @ Sat, 11 Dec 2021 06:52:18: #1 total tags in treatment: 6137645 INFO @ Sat, 11 Dec 2021 06:52:18: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:52:18: #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 06:52:18: #1 tags after filtering in treatment: 6137645 INFO @ Sat, 11 Dec 2021 06:52:18: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:52:18: #1 finished! INFO @ Sat, 11 Dec 2021 06:52:18: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:52:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:52:18: #2 number of paired peaks: 210 WARNING @ Sat, 11 Dec 2021 06:52:18: Fewer paired peaks (210) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 210 pairs to build model! INFO @ Sat, 11 Dec 2021 06:52:18: start model_add_line... INFO @ Sat, 11 Dec 2021 06:52:18: start X-correlation... INFO @ Sat, 11 Dec 2021 06:52:18: end of X-cor INFO @ Sat, 11 Dec 2021 06:52:18: #2 finished! INFO @ Sat, 11 Dec 2021 06:52:18: #2 predicted fragment length is 237 bps INFO @ Sat, 11 Dec 2021 06:52:18: #2 alternative fragment length(s) may be 237 bps INFO @ Sat, 11 Dec 2021 06:52:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8784757/SRX8784757.05_model.r INFO @ Sat, 11 Dec 2021 06:52:18: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:52:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:52:21: 2000000 INFO @ Sat, 11 Dec 2021 06:52:28: 3000000 INFO @ Sat, 11 Dec 2021 06:52:31: #3 Call peaks for each chromosome... 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 06:52:35: 4000000 INFO @ Sat, 11 Dec 2021 06:52:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8784757/SRX8784757.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8784757/SRX8784757.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8784757/SRX8784757.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8784757/SRX8784757.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 06:52:37: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:52:37: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:52:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8784757/SRX8784757.05_peaks.xls INFO @ Sat, 11 Dec 2021 06:52:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8784757/SRX8784757.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:52:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8784757/SRX8784757.05_summits.bed INFO @ Sat, 11 Dec 2021 06:52:37: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (2948 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:52:42: 5000000 INFO @ Sat, 11 Dec 2021 06:52:44: 1000000 INFO @ Sat, 11 Dec 2021 06:52:49: 6000000 INFO @ Sat, 11 Dec 2021 06:52:50: #1 tag size is determined as 95 bps INFO @ Sat, 11 Dec 2021 06:52:50: #1 tag size = 95 INFO @ Sat, 11 Dec 2021 06:52:50: #1 total tags in treatment: 6137645 INFO @ Sat, 11 Dec 2021 06:52:50: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:52:50: #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 06:52:50: #1 tags after filtering in treatment: 6137645 INFO @ Sat, 11 Dec 2021 06:52:50: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:52:50: #1 finished! INFO @ Sat, 11 Dec 2021 06:52:50: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:52:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:52:51: #2 number of paired peaks: 210 WARNING @ Sat, 11 Dec 2021 06:52:51: Fewer paired peaks (210) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 210 pairs to build model! INFO @ Sat, 11 Dec 2021 06:52:51: start model_add_line... INFO @ Sat, 11 Dec 2021 06:52:51: start X-correlation... INFO @ Sat, 11 Dec 2021 06:52:51: end of X-cor INFO @ Sat, 11 Dec 2021 06:52:51: #2 finished! INFO @ Sat, 11 Dec 2021 06:52:51: #2 predicted fragment length is 237 bps INFO @ Sat, 11 Dec 2021 06:52:51: #2 alternative fragment length(s) may be 237 bps INFO @ Sat, 11 Dec 2021 06:52:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8784757/SRX8784757.10_model.r INFO @ Sat, 11 Dec 2021 06:52:51: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:52:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:52:51: 2000000 INFO @ Sat, 11 Dec 2021 06:52:58: 3000000 INFO @ Sat, 11 Dec 2021 06:53:04: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:53:05: 4000000 INFO @ Sat, 11 Dec 2021 06:53:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8784757/SRX8784757.10_peaks.xls INFO @ Sat, 11 Dec 2021 06:53:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8784757/SRX8784757.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:53:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8784757/SRX8784757.10_summits.bed INFO @ Sat, 11 Dec 2021 06:53:10: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (788 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 06:53:12: 5000000 INFO @ Sat, 11 Dec 2021 06:53:18: 6000000 INFO @ Sat, 11 Dec 2021 06:53:19: #1 tag size is determined as 95 bps INFO @ Sat, 11 Dec 2021 06:53:19: #1 tag size = 95 INFO @ Sat, 11 Dec 2021 06:53:19: #1 total tags in treatment: 6137645 INFO @ Sat, 11 Dec 2021 06:53:19: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:53:19: #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 06:53:19: #1 tags after filtering in treatment: 6137645 INFO @ Sat, 11 Dec 2021 06:53:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:53:19: #1 finished! INFO @ Sat, 11 Dec 2021 06:53:19: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:53:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:53:20: #2 number of paired peaks: 210 WARNING @ Sat, 11 Dec 2021 06:53:20: Fewer paired peaks (210) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 210 pairs to build model! INFO @ Sat, 11 Dec 2021 06:53:20: start model_add_line... INFO @ Sat, 11 Dec 2021 06:53:20: start X-correlation... INFO @ Sat, 11 Dec 2021 06:53:20: end of X-cor INFO @ Sat, 11 Dec 2021 06:53:20: #2 finished! INFO @ Sat, 11 Dec 2021 06:53:20: #2 predicted fragment length is 237 bps INFO @ Sat, 11 Dec 2021 06:53:20: #2 alternative fragment length(s) may be 237 bps INFO @ Sat, 11 Dec 2021 06:53:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8784757/SRX8784757.20_model.r INFO @ Sat, 11 Dec 2021 06:53:20: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:53:20: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 06:53:33: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:53:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8784757/SRX8784757.20_peaks.xls INFO @ Sat, 11 Dec 2021 06:53:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8784757/SRX8784757.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:53:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8784757/SRX8784757.20_summits.bed INFO @ Sat, 11 Dec 2021 06:53:39: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (116 records, 4 fields): 1 millis CompletedMACS2peakCalling