Job ID = 14170393 SRX = SRX8689014 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 7301382 spots for SRR12174270/SRR12174270.sra Written 7301382 spots for SRR12174270/SRR12174270.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170796 ("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: 00:02:31 7301382 reads; of these: 7301382 (100.00%) were unpaired; of these: 168676 (2.31%) aligned 0 times 5107338 (69.95%) aligned exactly 1 time 2025368 (27.74%) aligned >1 times 97.69% overall alignment rate Time searching: 00:02:31 Overall time: 00:02:31 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] 268681 / 7132706 = 0.0377 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 06:44:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689014/SRX8689014.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689014/SRX8689014.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689014/SRX8689014.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689014/SRX8689014.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 06:44:54: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:44:54: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:44:59: 1000000 INFO @ Sat, 11 Dec 2021 06:45:05: 2000000 INFO @ Sat, 11 Dec 2021 06:45:10: 3000000 INFO @ Sat, 11 Dec 2021 06:45:15: 4000000 INFO @ Sat, 11 Dec 2021 06:45:21: 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 06:45:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689014/SRX8689014.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689014/SRX8689014.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689014/SRX8689014.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689014/SRX8689014.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 06:45:24: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:45:24: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:45:26: 6000000 INFO @ Sat, 11 Dec 2021 06:45:31: 1000000 INFO @ Sat, 11 Dec 2021 06:45:32: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:45:32: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:45:32: #1 total tags in treatment: 6864025 INFO @ Sat, 11 Dec 2021 06:45:32: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:45:32: #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 06:45:32: #1 tags after filtering in treatment: 6864025 INFO @ Sat, 11 Dec 2021 06:45:32: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:45:32: #1 finished! INFO @ Sat, 11 Dec 2021 06:45:32: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:45:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:45:32: #2 number of paired peaks: 177 WARNING @ Sat, 11 Dec 2021 06:45:32: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Sat, 11 Dec 2021 06:45:32: start model_add_line... INFO @ Sat, 11 Dec 2021 06:45:32: start X-correlation... INFO @ Sat, 11 Dec 2021 06:45:32: end of X-cor INFO @ Sat, 11 Dec 2021 06:45:32: #2 finished! INFO @ Sat, 11 Dec 2021 06:45:32: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Dec 2021 06:45:32: #2 alternative fragment length(s) may be 50 bps INFO @ Sat, 11 Dec 2021 06:45:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689014/SRX8689014.05_model.r WARNING @ Sat, 11 Dec 2021 06:45:32: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:45:32: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sat, 11 Dec 2021 06:45:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 06:45:32: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:45:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:45:37: 2000000 INFO @ Sat, 11 Dec 2021 06:45:43: 3000000 INFO @ Sat, 11 Dec 2021 06:45:46: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:45:50: 4000000 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 06:45:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689014/SRX8689014.05_peaks.xls INFO @ Sat, 11 Dec 2021 06:45:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689014/SRX8689014.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:45:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689014/SRX8689014.05_summits.bed INFO @ Sat, 11 Dec 2021 06:45:53: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (1175 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:45:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689014/SRX8689014.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689014/SRX8689014.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689014/SRX8689014.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689014/SRX8689014.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 06:45:54: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:45:54: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:45:56: 5000000 INFO @ Sat, 11 Dec 2021 06:46:01: 1000000 INFO @ Sat, 11 Dec 2021 06:46:03: 6000000 INFO @ Sat, 11 Dec 2021 06:46:08: 2000000 INFO @ Sat, 11 Dec 2021 06:46:08: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:46:08: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:46:08: #1 total tags in treatment: 6864025 INFO @ Sat, 11 Dec 2021 06:46:08: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:46:08: #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 06:46:08: #1 tags after filtering in treatment: 6864025 INFO @ Sat, 11 Dec 2021 06:46:08: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:46:08: #1 finished! INFO @ Sat, 11 Dec 2021 06:46:08: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:46:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:46:09: #2 number of paired peaks: 177 WARNING @ Sat, 11 Dec 2021 06:46:09: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Sat, 11 Dec 2021 06:46:09: start model_add_line... INFO @ Sat, 11 Dec 2021 06:46:09: start X-correlation... INFO @ Sat, 11 Dec 2021 06:46:09: end of X-cor INFO @ Sat, 11 Dec 2021 06:46:09: #2 finished! INFO @ Sat, 11 Dec 2021 06:46:09: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Dec 2021 06:46:09: #2 alternative fragment length(s) may be 50 bps INFO @ Sat, 11 Dec 2021 06:46:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689014/SRX8689014.10_model.r WARNING @ Sat, 11 Dec 2021 06:46:09: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:46:09: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sat, 11 Dec 2021 06:46:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 06:46:09: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:46:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:46:14: 3000000 INFO @ Sat, 11 Dec 2021 06:46:21: 4000000 INFO @ Sat, 11 Dec 2021 06:46:22: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 06:46:27: 5000000 INFO @ Sat, 11 Dec 2021 06:46:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689014/SRX8689014.10_peaks.xls INFO @ Sat, 11 Dec 2021 06:46:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689014/SRX8689014.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:46:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689014/SRX8689014.10_summits.bed INFO @ Sat, 11 Dec 2021 06:46:28: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (951 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:46:34: 6000000 INFO @ Sat, 11 Dec 2021 06:46:40: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:46:40: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:46:40: #1 total tags in treatment: 6864025 INFO @ Sat, 11 Dec 2021 06:46:40: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:46:40: #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 06:46:40: #1 tags after filtering in treatment: 6864025 INFO @ Sat, 11 Dec 2021 06:46:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:46:40: #1 finished! INFO @ Sat, 11 Dec 2021 06:46:40: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:46:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:46:40: #2 number of paired peaks: 177 WARNING @ Sat, 11 Dec 2021 06:46:40: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Sat, 11 Dec 2021 06:46:40: start model_add_line... INFO @ Sat, 11 Dec 2021 06:46:40: start X-correlation... INFO @ Sat, 11 Dec 2021 06:46:40: end of X-cor INFO @ Sat, 11 Dec 2021 06:46:40: #2 finished! INFO @ Sat, 11 Dec 2021 06:46:40: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Dec 2021 06:46:40: #2 alternative fragment length(s) may be 50 bps INFO @ Sat, 11 Dec 2021 06:46:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689014/SRX8689014.20_model.r WARNING @ Sat, 11 Dec 2021 06:46:40: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:46:40: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sat, 11 Dec 2021 06:46:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 06:46:40: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:46:40: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 06:46:53: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:47:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689014/SRX8689014.20_peaks.xls INFO @ Sat, 11 Dec 2021 06:47:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689014/SRX8689014.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:47:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689014/SRX8689014.20_summits.bed INFO @ Sat, 11 Dec 2021 06:47:00: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (632 records, 4 fields): 2 millis CompletedMACS2peakCalling