Job ID = 14170566 SRX = SRX8689098 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 5860406 spots for SRR12174356/SRR12174356.sra Written 5860406 spots for SRR12174356/SRR12174356.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170970 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:01:47 5860406 reads; of these: 5860406 (100.00%) were unpaired; of these: 166417 (2.84%) aligned 0 times 4497235 (76.74%) aligned exactly 1 time 1196754 (20.42%) aligned >1 times 97.16% overall alignment rate Time searching: 00:01:48 Overall time: 00:01:48 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] 215043 / 5693989 = 0.0378 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 07:20:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689098/SRX8689098.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689098/SRX8689098.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689098/SRX8689098.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689098/SRX8689098.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 07:20:25: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:20:25: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:20:30: 1000000 INFO @ Sat, 11 Dec 2021 07:20:36: 2000000 INFO @ Sat, 11 Dec 2021 07:20:42: 3000000 INFO @ Sat, 11 Dec 2021 07:20:47: 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 07:20:53: 5000000 INFO @ Sat, 11 Dec 2021 07:20:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689098/SRX8689098.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689098/SRX8689098.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689098/SRX8689098.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689098/SRX8689098.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 07:20:54: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:20:54: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:20:56: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:20:56: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:20:56: #1 total tags in treatment: 5478946 INFO @ Sat, 11 Dec 2021 07:20:56: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:20:56: #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 07:20:56: #1 tags after filtering in treatment: 5478946 INFO @ Sat, 11 Dec 2021 07:20:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:20:56: #1 finished! INFO @ Sat, 11 Dec 2021 07:20:56: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:20:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:20:56: #2 number of paired peaks: 212 WARNING @ Sat, 11 Dec 2021 07:20:56: Fewer paired peaks (212) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 212 pairs to build model! INFO @ Sat, 11 Dec 2021 07:20:56: start model_add_line... INFO @ Sat, 11 Dec 2021 07:20:56: start X-correlation... INFO @ Sat, 11 Dec 2021 07:20:56: end of X-cor INFO @ Sat, 11 Dec 2021 07:20:56: #2 finished! INFO @ Sat, 11 Dec 2021 07:20:56: #2 predicted fragment length is 51 bps INFO @ Sat, 11 Dec 2021 07:20:56: #2 alternative fragment length(s) may be 51 bps INFO @ Sat, 11 Dec 2021 07:20:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689098/SRX8689098.05_model.r WARNING @ Sat, 11 Dec 2021 07:20:56: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:20:56: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Sat, 11 Dec 2021 07:20:56: #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 07:20:56: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:20:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:21:00: 1000000 INFO @ Sat, 11 Dec 2021 07:21:06: 2000000 INFO @ Sat, 11 Dec 2021 07:21:07: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:21:11: 3000000 INFO @ Sat, 11 Dec 2021 07:21:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689098/SRX8689098.05_peaks.xls INFO @ Sat, 11 Dec 2021 07:21:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689098/SRX8689098.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:21:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689098/SRX8689098.05_summits.bed INFO @ Sat, 11 Dec 2021 07:21:13: Done! INFO @ Sat, 11 Dec 2021 07:21:17: 4000000 pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (1068 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 07:21:23: 5000000 INFO @ Sat, 11 Dec 2021 07:21:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689098/SRX8689098.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689098/SRX8689098.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689098/SRX8689098.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689098/SRX8689098.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 07:21:24: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:21:24: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:21:26: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:21:26: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:21:26: #1 total tags in treatment: 5478946 INFO @ Sat, 11 Dec 2021 07:21:26: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:21:26: #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 07:21:26: #1 tags after filtering in treatment: 5478946 INFO @ Sat, 11 Dec 2021 07:21:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:21:26: #1 finished! INFO @ Sat, 11 Dec 2021 07:21:26: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:21:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:21:26: #2 number of paired peaks: 212 WARNING @ Sat, 11 Dec 2021 07:21:26: Fewer paired peaks (212) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 212 pairs to build model! INFO @ Sat, 11 Dec 2021 07:21:26: start model_add_line... INFO @ Sat, 11 Dec 2021 07:21:26: start X-correlation... INFO @ Sat, 11 Dec 2021 07:21:26: end of X-cor INFO @ Sat, 11 Dec 2021 07:21:26: #2 finished! INFO @ Sat, 11 Dec 2021 07:21:26: #2 predicted fragment length is 51 bps INFO @ Sat, 11 Dec 2021 07:21:26: #2 alternative fragment length(s) may be 51 bps INFO @ Sat, 11 Dec 2021 07:21:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689098/SRX8689098.10_model.r WARNING @ Sat, 11 Dec 2021 07:21:26: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:21:26: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Sat, 11 Dec 2021 07:21:26: #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 07:21:26: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:21:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:21:30: 1000000 INFO @ Sat, 11 Dec 2021 07:21:36: 2000000 INFO @ Sat, 11 Dec 2021 07:21:38: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:21:42: 3000000 INFO @ Sat, 11 Dec 2021 07:21:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689098/SRX8689098.10_peaks.xls INFO @ Sat, 11 Dec 2021 07:21:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689098/SRX8689098.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:21:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689098/SRX8689098.10_summits.bed INFO @ Sat, 11 Dec 2021 07:21:44: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (827 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:21:48: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 07:21:54: 5000000 INFO @ Sat, 11 Dec 2021 07:21:57: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:21:57: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:21:57: #1 total tags in treatment: 5478946 INFO @ Sat, 11 Dec 2021 07:21:57: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:21:57: #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 07:21:57: #1 tags after filtering in treatment: 5478946 INFO @ Sat, 11 Dec 2021 07:21:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:21:57: #1 finished! INFO @ Sat, 11 Dec 2021 07:21:57: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:21:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:21:57: #2 number of paired peaks: 212 WARNING @ Sat, 11 Dec 2021 07:21:57: Fewer paired peaks (212) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 212 pairs to build model! INFO @ Sat, 11 Dec 2021 07:21:57: start model_add_line... INFO @ Sat, 11 Dec 2021 07:21:57: start X-correlation... INFO @ Sat, 11 Dec 2021 07:21:57: end of X-cor INFO @ Sat, 11 Dec 2021 07:21:57: #2 finished! INFO @ Sat, 11 Dec 2021 07:21:57: #2 predicted fragment length is 51 bps INFO @ Sat, 11 Dec 2021 07:21:57: #2 alternative fragment length(s) may be 51 bps INFO @ Sat, 11 Dec 2021 07:21:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689098/SRX8689098.20_model.r WARNING @ Sat, 11 Dec 2021 07:21:57: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:21:57: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Sat, 11 Dec 2021 07:21:57: #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 07:21:57: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:21:57: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 07:22:09: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:22:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689098/SRX8689098.20_peaks.xls INFO @ Sat, 11 Dec 2021 07:22:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689098/SRX8689098.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:22:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689098/SRX8689098.20_summits.bed INFO @ Sat, 11 Dec 2021 07:22:15: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (467 records, 4 fields): 1 millis CompletedMACS2peakCalling