Job ID = 14167992 SRX = SRX8688962 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 9381156 spots for SRR12174364/SRR12174364.sra Written 9381156 spots for SRR12174364/SRR12174364.sra fastq に変換しました。 bowtie でマッピング中... Your job 14168534 ("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: 00:03:07 9381156 reads; of these: 9381156 (100.00%) were unpaired; of these: 1844512 (19.66%) aligned 0 times 5151592 (54.91%) aligned exactly 1 time 2385052 (25.42%) aligned >1 times 80.34% overall alignment rate Time searching: 00:03:08 Overall time: 00:03:08 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] 887929 / 7536644 = 0.1178 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 @ Fri, 10 Dec 2021 14:16:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688962/SRX8688962.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688962/SRX8688962.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688962/SRX8688962.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688962/SRX8688962.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 @ Fri, 10 Dec 2021 14:16:34: #1 read tag files... INFO @ Fri, 10 Dec 2021 14:16:34: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 14:16:41: 1000000 INFO @ Fri, 10 Dec 2021 14:16:47: 2000000 INFO @ Fri, 10 Dec 2021 14:16:55: 3000000 INFO @ Fri, 10 Dec 2021 14:17:02: 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 @ Fri, 10 Dec 2021 14:17:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688962/SRX8688962.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688962/SRX8688962.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688962/SRX8688962.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688962/SRX8688962.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 @ Fri, 10 Dec 2021 14:17:04: #1 read tag files... INFO @ Fri, 10 Dec 2021 14:17:04: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 14:17:09: 5000000 INFO @ Fri, 10 Dec 2021 14:17:11: 1000000 INFO @ Fri, 10 Dec 2021 14:17:17: 6000000 INFO @ Fri, 10 Dec 2021 14:17:19: 2000000 INFO @ Fri, 10 Dec 2021 14:17:21: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 14:17:21: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 14:17:21: #1 total tags in treatment: 6648715 INFO @ Fri, 10 Dec 2021 14:17:21: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 14:17:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 14:17:21: #1 tags after filtering in treatment: 6648715 INFO @ Fri, 10 Dec 2021 14:17:21: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 14:17:21: #1 finished! INFO @ Fri, 10 Dec 2021 14:17:21: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 14:17:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 14:17:22: #2 number of paired peaks: 432 WARNING @ Fri, 10 Dec 2021 14:17:22: Fewer paired peaks (432) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 432 pairs to build model! INFO @ Fri, 10 Dec 2021 14:17:22: start model_add_line... INFO @ Fri, 10 Dec 2021 14:17:22: start X-correlation... INFO @ Fri, 10 Dec 2021 14:17:22: end of X-cor INFO @ Fri, 10 Dec 2021 14:17:22: #2 finished! INFO @ Fri, 10 Dec 2021 14:17:22: #2 predicted fragment length is 49 bps INFO @ Fri, 10 Dec 2021 14:17:22: #2 alternative fragment length(s) may be 49 bps INFO @ Fri, 10 Dec 2021 14:17:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688962/SRX8688962.05_model.r WARNING @ Fri, 10 Dec 2021 14:17:22: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 14:17:22: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Fri, 10 Dec 2021 14:17:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 14:17:22: #3 Call peaks... INFO @ Fri, 10 Dec 2021 14:17:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 14:17:26: 3000000 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 @ Fri, 10 Dec 2021 14:17:33: 4000000 INFO @ Fri, 10 Dec 2021 14:17:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688962/SRX8688962.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688962/SRX8688962.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688962/SRX8688962.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688962/SRX8688962.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 @ Fri, 10 Dec 2021 14:17:34: #1 read tag files... INFO @ Fri, 10 Dec 2021 14:17:34: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 14:17:38: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 14:17:41: 5000000 INFO @ Fri, 10 Dec 2021 14:17:41: 1000000 INFO @ Fri, 10 Dec 2021 14:17:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688962/SRX8688962.05_peaks.xls INFO @ Fri, 10 Dec 2021 14:17:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688962/SRX8688962.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 14:17:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688962/SRX8688962.05_summits.bed INFO @ Fri, 10 Dec 2021 14:17:46: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1427 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 14:17:48: 2000000 INFO @ Fri, 10 Dec 2021 14:17:49: 6000000 INFO @ Fri, 10 Dec 2021 14:17:54: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 14:17:54: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 14:17:54: #1 total tags in treatment: 6648715 INFO @ Fri, 10 Dec 2021 14:17:54: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 14:17:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 14:17:54: #1 tags after filtering in treatment: 6648715 INFO @ Fri, 10 Dec 2021 14:17:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 14:17:54: #1 finished! INFO @ Fri, 10 Dec 2021 14:17:54: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 14:17:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 14:17:55: #2 number of paired peaks: 432 WARNING @ Fri, 10 Dec 2021 14:17:55: Fewer paired peaks (432) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 432 pairs to build model! INFO @ Fri, 10 Dec 2021 14:17:55: start model_add_line... INFO @ Fri, 10 Dec 2021 14:17:55: start X-correlation... INFO @ Fri, 10 Dec 2021 14:17:55: end of X-cor INFO @ Fri, 10 Dec 2021 14:17:55: #2 finished! INFO @ Fri, 10 Dec 2021 14:17:55: #2 predicted fragment length is 49 bps INFO @ Fri, 10 Dec 2021 14:17:55: #2 alternative fragment length(s) may be 49 bps INFO @ Fri, 10 Dec 2021 14:17:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688962/SRX8688962.10_model.r WARNING @ Fri, 10 Dec 2021 14:17:55: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 14:17:55: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Fri, 10 Dec 2021 14:17:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 14:17:55: #3 Call peaks... INFO @ Fri, 10 Dec 2021 14:17:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 14:17:56: 3000000 INFO @ Fri, 10 Dec 2021 14:18:02: 4000000 INFO @ Fri, 10 Dec 2021 14:18:09: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 14:18:10: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 14:18:16: 6000000 INFO @ Fri, 10 Dec 2021 14:18:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688962/SRX8688962.10_peaks.xls INFO @ Fri, 10 Dec 2021 14:18:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688962/SRX8688962.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 14:18:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688962/SRX8688962.10_summits.bed INFO @ Fri, 10 Dec 2021 14:18:18: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (1166 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 14:18:21: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 14:18:21: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 14:18:21: #1 total tags in treatment: 6648715 INFO @ Fri, 10 Dec 2021 14:18:21: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 14:18:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 14:18:21: #1 tags after filtering in treatment: 6648715 INFO @ Fri, 10 Dec 2021 14:18:21: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 14:18:21: #1 finished! INFO @ Fri, 10 Dec 2021 14:18:21: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 14:18:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 14:18:21: #2 number of paired peaks: 432 WARNING @ Fri, 10 Dec 2021 14:18:21: Fewer paired peaks (432) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 432 pairs to build model! INFO @ Fri, 10 Dec 2021 14:18:21: start model_add_line... INFO @ Fri, 10 Dec 2021 14:18:21: start X-correlation... INFO @ Fri, 10 Dec 2021 14:18:21: end of X-cor INFO @ Fri, 10 Dec 2021 14:18:21: #2 finished! INFO @ Fri, 10 Dec 2021 14:18:21: #2 predicted fragment length is 49 bps INFO @ Fri, 10 Dec 2021 14:18:21: #2 alternative fragment length(s) may be 49 bps INFO @ Fri, 10 Dec 2021 14:18:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688962/SRX8688962.20_model.r WARNING @ Fri, 10 Dec 2021 14:18:21: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 14:18:21: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Fri, 10 Dec 2021 14:18:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 14:18:21: #3 Call peaks... INFO @ Fri, 10 Dec 2021 14:18:21: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 14:18:36: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 14:18:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688962/SRX8688962.20_peaks.xls INFO @ Fri, 10 Dec 2021 14:18:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688962/SRX8688962.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 14:18:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688962/SRX8688962.20_summits.bed INFO @ Fri, 10 Dec 2021 14:18:44: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (889 records, 4 fields): 3 millis CompletedMACS2peakCalling