Job ID = 14170567 SRX = SRX8689099 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 5797892 spots for SRR12174357/SRR12174357.sra Written 5797892 spots for SRR12174357/SRR12174357.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170971 ("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: 00:01:55 5797892 reads; of these: 5797892 (100.00%) were unpaired; of these: 199410 (3.44%) aligned 0 times 4185273 (72.19%) aligned exactly 1 time 1413209 (24.37%) aligned >1 times 96.56% overall alignment rate Time searching: 00:01:56 Overall time: 00:01:56 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] 231614 / 5598482 = 0.0414 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 07:20:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689099/SRX8689099.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689099/SRX8689099.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689099/SRX8689099.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689099/SRX8689099.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 07:20:31: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:20:31: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:20:37: 1000000 INFO @ Sat, 11 Dec 2021 07:20:42: 2000000 INFO @ Sat, 11 Dec 2021 07:20:48: 3000000 INFO @ Sat, 11 Dec 2021 07:20:53: 4000000 INFO @ Sat, 11 Dec 2021 07:20:59: 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 07:21:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689099/SRX8689099.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689099/SRX8689099.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689099/SRX8689099.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689099/SRX8689099.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 07:21:01: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:21:01: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:21:01: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:21:01: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:21:01: #1 total tags in treatment: 5366868 INFO @ Sat, 11 Dec 2021 07:21:01: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:21:01: #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 07:21:01: #1 tags after filtering in treatment: 5366868 INFO @ Sat, 11 Dec 2021 07:21:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:21:01: #1 finished! INFO @ Sat, 11 Dec 2021 07:21:01: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:21:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:21:02: #2 number of paired peaks: 281 WARNING @ Sat, 11 Dec 2021 07:21:02: Fewer paired peaks (281) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 281 pairs to build model! INFO @ Sat, 11 Dec 2021 07:21:02: start model_add_line... INFO @ Sat, 11 Dec 2021 07:21:02: start X-correlation... INFO @ Sat, 11 Dec 2021 07:21:02: end of X-cor INFO @ Sat, 11 Dec 2021 07:21:02: #2 finished! INFO @ Sat, 11 Dec 2021 07:21:02: #2 predicted fragment length is 51 bps INFO @ Sat, 11 Dec 2021 07:21:02: #2 alternative fragment length(s) may be 51 bps INFO @ Sat, 11 Dec 2021 07:21:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689099/SRX8689099.05_model.r WARNING @ Sat, 11 Dec 2021 07:21:02: #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 07:21:02: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Sat, 11 Dec 2021 07:21:02: #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 07:21:02: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:21:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:21:07: 1000000 INFO @ Sat, 11 Dec 2021 07:21:12: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:21:13: 2000000 INFO @ Sat, 11 Dec 2021 07:21:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689099/SRX8689099.05_peaks.xls INFO @ Sat, 11 Dec 2021 07:21:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689099/SRX8689099.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:21:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689099/SRX8689099.05_summits.bed INFO @ Sat, 11 Dec 2021 07:21:18: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1152 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:21:18: 3000000 INFO @ Sat, 11 Dec 2021 07:21:24: 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 07:21:30: 5000000 INFO @ Sat, 11 Dec 2021 07:21:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689099/SRX8689099.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689099/SRX8689099.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689099/SRX8689099.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689099/SRX8689099.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 07:21:31: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:21:31: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:21:32: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:21:32: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:21:32: #1 total tags in treatment: 5366868 INFO @ Sat, 11 Dec 2021 07:21:32: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:21:32: #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 07:21:32: #1 tags after filtering in treatment: 5366868 INFO @ Sat, 11 Dec 2021 07:21:32: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:21:32: #1 finished! INFO @ Sat, 11 Dec 2021 07:21:32: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:21:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:21:32: #2 number of paired peaks: 281 WARNING @ Sat, 11 Dec 2021 07:21:32: Fewer paired peaks (281) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 281 pairs to build model! INFO @ Sat, 11 Dec 2021 07:21:32: start model_add_line... INFO @ Sat, 11 Dec 2021 07:21:32: start X-correlation... INFO @ Sat, 11 Dec 2021 07:21:32: end of X-cor INFO @ Sat, 11 Dec 2021 07:21:32: #2 finished! INFO @ Sat, 11 Dec 2021 07:21:32: #2 predicted fragment length is 51 bps INFO @ Sat, 11 Dec 2021 07:21:32: #2 alternative fragment length(s) may be 51 bps INFO @ Sat, 11 Dec 2021 07:21:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689099/SRX8689099.10_model.r WARNING @ Sat, 11 Dec 2021 07:21:32: #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 07:21:32: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Sat, 11 Dec 2021 07:21:32: #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 07:21:32: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:21:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:21:38: 1000000 INFO @ Sat, 11 Dec 2021 07:21:43: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:21:45: 2000000 INFO @ Sat, 11 Dec 2021 07:21:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689099/SRX8689099.10_peaks.xls INFO @ Sat, 11 Dec 2021 07:21:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689099/SRX8689099.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:21:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689099/SRX8689099.10_summits.bed INFO @ Sat, 11 Dec 2021 07:21:49: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (920 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:21:52: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 07:21:59: 4000000 INFO @ Sat, 11 Dec 2021 07:22:06: 5000000 INFO @ Sat, 11 Dec 2021 07:22:08: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:22:08: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:22:08: #1 total tags in treatment: 5366868 INFO @ Sat, 11 Dec 2021 07:22:08: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:22:08: #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 07:22:08: #1 tags after filtering in treatment: 5366868 INFO @ Sat, 11 Dec 2021 07:22:08: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:22:08: #1 finished! INFO @ Sat, 11 Dec 2021 07:22:08: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:22:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:22:09: #2 number of paired peaks: 281 WARNING @ Sat, 11 Dec 2021 07:22:09: Fewer paired peaks (281) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 281 pairs to build model! INFO @ Sat, 11 Dec 2021 07:22:09: start model_add_line... INFO @ Sat, 11 Dec 2021 07:22:09: start X-correlation... INFO @ Sat, 11 Dec 2021 07:22:09: end of X-cor INFO @ Sat, 11 Dec 2021 07:22:09: #2 finished! INFO @ Sat, 11 Dec 2021 07:22:09: #2 predicted fragment length is 51 bps INFO @ Sat, 11 Dec 2021 07:22:09: #2 alternative fragment length(s) may be 51 bps INFO @ Sat, 11 Dec 2021 07:22:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689099/SRX8689099.20_model.r WARNING @ Sat, 11 Dec 2021 07:22:09: #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 07:22:09: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Sat, 11 Dec 2021 07:22:09: #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 07:22:09: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:22:09: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 07:22:20: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:22:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689099/SRX8689099.20_peaks.xls INFO @ Sat, 11 Dec 2021 07:22:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689099/SRX8689099.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:22:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689099/SRX8689099.20_summits.bed INFO @ Sat, 11 Dec 2021 07:22:26: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (562 records, 4 fields): 1 millis CompletedMACS2peakCalling