Job ID = 14171157 SRX = SRX9986105 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 20164486 spots for SRR13591499/SRR13591499.sra Written 20164486 spots for SRR13591499/SRR13591499.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171662 ("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: 00:20:23 20164486 reads; of these: 20164486 (100.00%) were unpaired; of these: 1789737 (8.88%) aligned 0 times 6959579 (34.51%) aligned exactly 1 time 11415170 (56.61%) aligned >1 times 91.12% overall alignment rate Time searching: 00:20:23 Overall time: 00:20:23 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 8 files... [bam_rmdupse_core] 11840218 / 18374749 = 0.6444 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 10:36:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986105/SRX9986105.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986105/SRX9986105.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986105/SRX9986105.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986105/SRX9986105.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 10:36:38: #1 read tag files... INFO @ Sat, 11 Dec 2021 10:36:38: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 10:36:43: 1000000 INFO @ Sat, 11 Dec 2021 10:36:49: 2000000 INFO @ Sat, 11 Dec 2021 10:36:55: 3000000 INFO @ Sat, 11 Dec 2021 10:37:00: 4000000 INFO @ Sat, 11 Dec 2021 10:37:06: 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 @ Sat, 11 Dec 2021 10:37:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986105/SRX9986105.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986105/SRX9986105.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986105/SRX9986105.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986105/SRX9986105.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 10:37:08: #1 read tag files... INFO @ Sat, 11 Dec 2021 10:37:08: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 10:37:12: 6000000 INFO @ Sat, 11 Dec 2021 10:37:15: 1000000 INFO @ Sat, 11 Dec 2021 10:37:16: #1 tag size is determined as 58 bps INFO @ Sat, 11 Dec 2021 10:37:16: #1 tag size = 58 INFO @ Sat, 11 Dec 2021 10:37:16: #1 total tags in treatment: 6534531 INFO @ Sat, 11 Dec 2021 10:37:16: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:37:16: #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 10:37:16: #1 tags after filtering in treatment: 6534531 INFO @ Sat, 11 Dec 2021 10:37:16: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 10:37:16: #1 finished! INFO @ Sat, 11 Dec 2021 10:37:16: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:37:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 10:37:16: #2 number of paired peaks: 412 WARNING @ Sat, 11 Dec 2021 10:37:16: Fewer paired peaks (412) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 412 pairs to build model! INFO @ Sat, 11 Dec 2021 10:37:16: start model_add_line... INFO @ Sat, 11 Dec 2021 10:37:16: start X-correlation... INFO @ Sat, 11 Dec 2021 10:37:16: end of X-cor INFO @ Sat, 11 Dec 2021 10:37:16: #2 finished! INFO @ Sat, 11 Dec 2021 10:37:16: #2 predicted fragment length is 187 bps INFO @ Sat, 11 Dec 2021 10:37:16: #2 alternative fragment length(s) may be 187 bps INFO @ Sat, 11 Dec 2021 10:37:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986105/SRX9986105.05_model.r INFO @ Sat, 11 Dec 2021 10:37:16: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:37:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 10:37:22: 2000000 INFO @ Sat, 11 Dec 2021 10:37:29: 3000000 INFO @ Sat, 11 Dec 2021 10:37:30: #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 10:37:36: 4000000 INFO @ Sat, 11 Dec 2021 10:37:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986105/SRX9986105.05_peaks.xls INFO @ Sat, 11 Dec 2021 10:37:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986105/SRX9986105.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:37:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986105/SRX9986105.05_summits.bed INFO @ Sat, 11 Dec 2021 10:37:37: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10484 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 10:37:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986105/SRX9986105.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986105/SRX9986105.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986105/SRX9986105.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986105/SRX9986105.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 10:37:38: #1 read tag files... INFO @ Sat, 11 Dec 2021 10:37:38: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 10:37:43: 5000000 INFO @ Sat, 11 Dec 2021 10:37:45: 1000000 INFO @ Sat, 11 Dec 2021 10:37:51: 6000000 INFO @ Sat, 11 Dec 2021 10:37:52: 2000000 INFO @ Sat, 11 Dec 2021 10:37:55: #1 tag size is determined as 58 bps INFO @ Sat, 11 Dec 2021 10:37:55: #1 tag size = 58 INFO @ Sat, 11 Dec 2021 10:37:55: #1 total tags in treatment: 6534531 INFO @ Sat, 11 Dec 2021 10:37:55: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:37:55: #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 10:37:55: #1 tags after filtering in treatment: 6534531 INFO @ Sat, 11 Dec 2021 10:37:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 10:37:55: #1 finished! INFO @ Sat, 11 Dec 2021 10:37:55: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:37:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 10:37:55: #2 number of paired peaks: 412 WARNING @ Sat, 11 Dec 2021 10:37:55: Fewer paired peaks (412) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 412 pairs to build model! INFO @ Sat, 11 Dec 2021 10:37:55: start model_add_line... INFO @ Sat, 11 Dec 2021 10:37:55: start X-correlation... INFO @ Sat, 11 Dec 2021 10:37:55: end of X-cor INFO @ Sat, 11 Dec 2021 10:37:55: #2 finished! INFO @ Sat, 11 Dec 2021 10:37:55: #2 predicted fragment length is 187 bps INFO @ Sat, 11 Dec 2021 10:37:55: #2 alternative fragment length(s) may be 187 bps INFO @ Sat, 11 Dec 2021 10:37:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986105/SRX9986105.10_model.r INFO @ Sat, 11 Dec 2021 10:37:55: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:37:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 10:37:59: 3000000 INFO @ Sat, 11 Dec 2021 10:38:06: 4000000 INFO @ Sat, 11 Dec 2021 10:38:09: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 10:38:13: 5000000 INFO @ Sat, 11 Dec 2021 10:38:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986105/SRX9986105.10_peaks.xls INFO @ Sat, 11 Dec 2021 10:38:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986105/SRX9986105.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:38:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986105/SRX9986105.10_summits.bed INFO @ Sat, 11 Dec 2021 10:38:16: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3879 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 10:38:20: 6000000 INFO @ Sat, 11 Dec 2021 10:38:23: #1 tag size is determined as 58 bps INFO @ Sat, 11 Dec 2021 10:38:23: #1 tag size = 58 INFO @ Sat, 11 Dec 2021 10:38:23: #1 total tags in treatment: 6534531 INFO @ Sat, 11 Dec 2021 10:38:23: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:38:23: #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 10:38:24: #1 tags after filtering in treatment: 6534531 INFO @ Sat, 11 Dec 2021 10:38:24: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 10:38:24: #1 finished! INFO @ Sat, 11 Dec 2021 10:38:24: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:38:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 10:38:24: #2 number of paired peaks: 412 WARNING @ Sat, 11 Dec 2021 10:38:24: Fewer paired peaks (412) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 412 pairs to build model! INFO @ Sat, 11 Dec 2021 10:38:24: start model_add_line... INFO @ Sat, 11 Dec 2021 10:38:24: start X-correlation... INFO @ Sat, 11 Dec 2021 10:38:24: end of X-cor INFO @ Sat, 11 Dec 2021 10:38:24: #2 finished! INFO @ Sat, 11 Dec 2021 10:38:24: #2 predicted fragment length is 187 bps INFO @ Sat, 11 Dec 2021 10:38:24: #2 alternative fragment length(s) may be 187 bps INFO @ Sat, 11 Dec 2021 10:38:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986105/SRX9986105.20_model.r INFO @ Sat, 11 Dec 2021 10:38:24: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:38:24: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 10:38:38: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 10:38:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986105/SRX9986105.20_peaks.xls INFO @ Sat, 11 Dec 2021 10:38:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986105/SRX9986105.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:38:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986105/SRX9986105.20_summits.bed INFO @ Sat, 11 Dec 2021 10:38:45: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (702 records, 4 fields): 2 millis CompletedMACS2peakCalling