Job ID = 14170454 SRX = SRX8689027 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 7995816 spots for SRR12174332/SRR12174332.sra Written 7995816 spots for SRR12174332/SRR12174332.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170853 ("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: 00:03:06 7995816 reads; of these: 7995816 (100.00%) were unpaired; of these: 213706 (2.67%) aligned 0 times 5123318 (64.07%) aligned exactly 1 time 2658792 (33.25%) aligned >1 times 97.33% overall alignment rate Time searching: 00:03:06 Overall time: 00:03:06 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] 517520 / 7782110 = 0.0665 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 06:53:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689027/SRX8689027.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689027/SRX8689027.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689027/SRX8689027.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689027/SRX8689027.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 06:53:51: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:53:51: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:53:56: 1000000 INFO @ Sat, 11 Dec 2021 06:54:02: 2000000 INFO @ Sat, 11 Dec 2021 06:54:07: 3000000 INFO @ Sat, 11 Dec 2021 06:54:13: 4000000 INFO @ Sat, 11 Dec 2021 06:54:19: 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 06:54:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689027/SRX8689027.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689027/SRX8689027.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689027/SRX8689027.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689027/SRX8689027.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 06:54:21: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:54:21: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:54:25: 6000000 INFO @ Sat, 11 Dec 2021 06:54:28: 1000000 INFO @ Sat, 11 Dec 2021 06:54:31: 7000000 INFO @ Sat, 11 Dec 2021 06:54:33: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:54:33: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:54:33: #1 total tags in treatment: 7264590 INFO @ Sat, 11 Dec 2021 06:54:33: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:54:33: #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 06:54:33: #1 tags after filtering in treatment: 7264590 INFO @ Sat, 11 Dec 2021 06:54:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:54:33: #1 finished! INFO @ Sat, 11 Dec 2021 06:54:33: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:54:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:54:34: #2 number of paired peaks: 493 WARNING @ Sat, 11 Dec 2021 06:54:34: Fewer paired peaks (493) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 493 pairs to build model! INFO @ Sat, 11 Dec 2021 06:54:34: start model_add_line... INFO @ Sat, 11 Dec 2021 06:54:34: start X-correlation... INFO @ Sat, 11 Dec 2021 06:54:34: end of X-cor INFO @ Sat, 11 Dec 2021 06:54:34: #2 finished! INFO @ Sat, 11 Dec 2021 06:54:34: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Dec 2021 06:54:34: #2 alternative fragment length(s) may be 50 bps INFO @ Sat, 11 Dec 2021 06:54:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689027/SRX8689027.05_model.r WARNING @ Sat, 11 Dec 2021 06:54:34: #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 06:54:34: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sat, 11 Dec 2021 06:54:34: #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 06:54:34: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:54:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:54:35: 2000000 INFO @ Sat, 11 Dec 2021 06:54:42: 3000000 INFO @ Sat, 11 Dec 2021 06:54:49: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:54:49: 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 06:54:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689027/SRX8689027.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689027/SRX8689027.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689027/SRX8689027.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689027/SRX8689027.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 06:54:51: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:54:51: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:54:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689027/SRX8689027.05_peaks.xls INFO @ Sat, 11 Dec 2021 06:54:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689027/SRX8689027.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:54:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689027/SRX8689027.05_summits.bed INFO @ Sat, 11 Dec 2021 06:54:56: Done! INFO @ Sat, 11 Dec 2021 06:54:56: 5000000 pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1550 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:54:58: 1000000 INFO @ Sat, 11 Dec 2021 06:55:03: 6000000 INFO @ Sat, 11 Dec 2021 06:55:04: 2000000 INFO @ Sat, 11 Dec 2021 06:55:11: 7000000 INFO @ Sat, 11 Dec 2021 06:55:11: 3000000 INFO @ Sat, 11 Dec 2021 06:55:12: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:55:12: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:55:12: #1 total tags in treatment: 7264590 INFO @ Sat, 11 Dec 2021 06:55:12: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:55:12: #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 06:55:12: #1 tags after filtering in treatment: 7264590 INFO @ Sat, 11 Dec 2021 06:55:12: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:55:12: #1 finished! INFO @ Sat, 11 Dec 2021 06:55:12: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:55:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:55:13: #2 number of paired peaks: 493 WARNING @ Sat, 11 Dec 2021 06:55:13: Fewer paired peaks (493) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 493 pairs to build model! INFO @ Sat, 11 Dec 2021 06:55:13: start model_add_line... INFO @ Sat, 11 Dec 2021 06:55:13: start X-correlation... INFO @ Sat, 11 Dec 2021 06:55:13: end of X-cor INFO @ Sat, 11 Dec 2021 06:55:13: #2 finished! INFO @ Sat, 11 Dec 2021 06:55:13: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Dec 2021 06:55:13: #2 alternative fragment length(s) may be 50 bps INFO @ Sat, 11 Dec 2021 06:55:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689027/SRX8689027.10_model.r WARNING @ Sat, 11 Dec 2021 06:55:13: #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 06:55:13: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sat, 11 Dec 2021 06:55:13: #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 06:55:13: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:55:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:55:17: 4000000 INFO @ Sat, 11 Dec 2021 06:55:23: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 06:55:27: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:55:29: 6000000 INFO @ Sat, 11 Dec 2021 06:55:34: 7000000 INFO @ Sat, 11 Dec 2021 06:55:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689027/SRX8689027.10_peaks.xls INFO @ Sat, 11 Dec 2021 06:55:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689027/SRX8689027.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:55:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689027/SRX8689027.10_summits.bed INFO @ Sat, 11 Dec 2021 06:55:35: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (1294 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:55:36: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:55:36: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:55:36: #1 total tags in treatment: 7264590 INFO @ Sat, 11 Dec 2021 06:55:36: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:55:36: #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 06:55:36: #1 tags after filtering in treatment: 7264590 INFO @ Sat, 11 Dec 2021 06:55:36: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:55:36: #1 finished! INFO @ Sat, 11 Dec 2021 06:55:36: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:55:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:55:36: #2 number of paired peaks: 493 WARNING @ Sat, 11 Dec 2021 06:55:36: Fewer paired peaks (493) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 493 pairs to build model! INFO @ Sat, 11 Dec 2021 06:55:36: start model_add_line... INFO @ Sat, 11 Dec 2021 06:55:36: start X-correlation... INFO @ Sat, 11 Dec 2021 06:55:36: end of X-cor INFO @ Sat, 11 Dec 2021 06:55:36: #2 finished! INFO @ Sat, 11 Dec 2021 06:55:36: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Dec 2021 06:55:36: #2 alternative fragment length(s) may be 50 bps INFO @ Sat, 11 Dec 2021 06:55:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689027/SRX8689027.20_model.r WARNING @ Sat, 11 Dec 2021 06:55:36: #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 06:55:36: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sat, 11 Dec 2021 06:55:36: #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 06:55:36: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:55:36: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 06:55:51: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:55:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689027/SRX8689027.20_peaks.xls INFO @ Sat, 11 Dec 2021 06:55:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689027/SRX8689027.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:55:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689027/SRX8689027.20_summits.bed INFO @ Sat, 11 Dec 2021 06:55:58: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1002 records, 4 fields): 2 millis CompletedMACS2peakCalling