Job ID = 6626633 SRX = SRX7262568 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 88583966 spots for SRR10582195/SRR10582195.sra Written 88583966 spots for SRR10582195/SRR10582195.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626918 ("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: 00:15:07 88583966 reads; of these: 88583966 (100.00%) were unpaired; of these: 80762990 (91.17%) aligned 0 times 5705512 (6.44%) aligned exactly 1 time 2115464 (2.39%) aligned >1 times 8.83% overall alignment rate Time searching: 00:15:07 Overall time: 00:15:07 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] 1258652 / 7820976 = 0.1609 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 08:27:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7262568/SRX7262568.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7262568/SRX7262568.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7262568/SRX7262568.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7262568/SRX7262568.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 @ Tue, 14 Jul 2020 08:27:36: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:27:36: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:27:42: 1000000 INFO @ Tue, 14 Jul 2020 08:27:48: 2000000 INFO @ Tue, 14 Jul 2020 08:27:54: 3000000 INFO @ Tue, 14 Jul 2020 08:28:00: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 08:28:07: 5000000 INFO @ Tue, 14 Jul 2020 08:28:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7262568/SRX7262568.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7262568/SRX7262568.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7262568/SRX7262568.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7262568/SRX7262568.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 @ Tue, 14 Jul 2020 08:28:07: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:28:07: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:28:13: 6000000 INFO @ Tue, 14 Jul 2020 08:28:13: 1000000 INFO @ Tue, 14 Jul 2020 08:28:16: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:28:16: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:28:16: #1 total tags in treatment: 6562324 INFO @ Tue, 14 Jul 2020 08:28:16: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:28:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:28:16: #1 tags after filtering in treatment: 6562324 INFO @ Tue, 14 Jul 2020 08:28:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:28:16: #1 finished! INFO @ Tue, 14 Jul 2020 08:28:16: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:28:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:28:17: #2 number of paired peaks: 1356 INFO @ Tue, 14 Jul 2020 08:28:17: start model_add_line... INFO @ Tue, 14 Jul 2020 08:28:17: start X-correlation... INFO @ Tue, 14 Jul 2020 08:28:17: end of X-cor INFO @ Tue, 14 Jul 2020 08:28:17: #2 finished! INFO @ Tue, 14 Jul 2020 08:28:17: #2 predicted fragment length is 78 bps INFO @ Tue, 14 Jul 2020 08:28:17: #2 alternative fragment length(s) may be 4,78,593 bps INFO @ Tue, 14 Jul 2020 08:28:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7262568/SRX7262568.05_model.r WARNING @ Tue, 14 Jul 2020 08:28:17: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:28:17: #2 You may need to consider one of the other alternative d(s): 4,78,593 WARNING @ Tue, 14 Jul 2020 08:28:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 08:28:17: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:28:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:28:19: 2000000 INFO @ Tue, 14 Jul 2020 08:28:26: 3000000 INFO @ Tue, 14 Jul 2020 08:28:32: 4000000 INFO @ Tue, 14 Jul 2020 08:28:32: #3 Call peaks for each chromosome... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 08:28:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7262568/SRX7262568.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7262568/SRX7262568.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7262568/SRX7262568.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7262568/SRX7262568.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 @ Tue, 14 Jul 2020 08:28:36: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:28:36: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:28:38: 5000000 INFO @ Tue, 14 Jul 2020 08:28:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7262568/SRX7262568.05_peaks.xls INFO @ Tue, 14 Jul 2020 08:28:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7262568/SRX7262568.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:28:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7262568/SRX7262568.05_summits.bed INFO @ Tue, 14 Jul 2020 08:28:40: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1653 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:28:42: 1000000 INFO @ Tue, 14 Jul 2020 08:28:44: 6000000 INFO @ Tue, 14 Jul 2020 08:28:47: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:28:47: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:28:47: #1 total tags in treatment: 6562324 INFO @ Tue, 14 Jul 2020 08:28:47: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:28:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:28:48: #1 tags after filtering in treatment: 6562324 INFO @ Tue, 14 Jul 2020 08:28:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:28:48: #1 finished! INFO @ Tue, 14 Jul 2020 08:28:48: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:28:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:28:48: #2 number of paired peaks: 1356 INFO @ Tue, 14 Jul 2020 08:28:48: start model_add_line... INFO @ Tue, 14 Jul 2020 08:28:48: start X-correlation... INFO @ Tue, 14 Jul 2020 08:28:48: end of X-cor INFO @ Tue, 14 Jul 2020 08:28:48: #2 finished! INFO @ Tue, 14 Jul 2020 08:28:48: #2 predicted fragment length is 78 bps INFO @ Tue, 14 Jul 2020 08:28:48: #2 alternative fragment length(s) may be 4,78,593 bps INFO @ Tue, 14 Jul 2020 08:28:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7262568/SRX7262568.10_model.r WARNING @ Tue, 14 Jul 2020 08:28:48: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:28:48: #2 You may need to consider one of the other alternative d(s): 4,78,593 WARNING @ Tue, 14 Jul 2020 08:28:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 08:28:48: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:28:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:28:49: 2000000 INFO @ Tue, 14 Jul 2020 08:28:55: 3000000 INFO @ Tue, 14 Jul 2020 08:29:01: 4000000 INFO @ Tue, 14 Jul 2020 08:29:03: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:29:07: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 08:29:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7262568/SRX7262568.10_peaks.xls INFO @ Tue, 14 Jul 2020 08:29:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7262568/SRX7262568.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:29:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7262568/SRX7262568.10_summits.bed INFO @ Tue, 14 Jul 2020 08:29:10: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (920 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:29:13: 6000000 INFO @ Tue, 14 Jul 2020 08:29:17: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:29:17: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:29:17: #1 total tags in treatment: 6562324 INFO @ Tue, 14 Jul 2020 08:29:17: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:29:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:29:17: #1 tags after filtering in treatment: 6562324 INFO @ Tue, 14 Jul 2020 08:29:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:29:17: #1 finished! INFO @ Tue, 14 Jul 2020 08:29:17: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:29:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:29:17: #2 number of paired peaks: 1356 INFO @ Tue, 14 Jul 2020 08:29:17: start model_add_line... INFO @ Tue, 14 Jul 2020 08:29:17: start X-correlation... INFO @ Tue, 14 Jul 2020 08:29:17: end of X-cor INFO @ Tue, 14 Jul 2020 08:29:17: #2 finished! INFO @ Tue, 14 Jul 2020 08:29:17: #2 predicted fragment length is 78 bps INFO @ Tue, 14 Jul 2020 08:29:17: #2 alternative fragment length(s) may be 4,78,593 bps INFO @ Tue, 14 Jul 2020 08:29:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7262568/SRX7262568.20_model.r WARNING @ Tue, 14 Jul 2020 08:29:17: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:29:17: #2 You may need to consider one of the other alternative d(s): 4,78,593 WARNING @ Tue, 14 Jul 2020 08:29:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 08:29:17: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:29:17: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 08:29:33: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:29:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7262568/SRX7262568.20_peaks.xls INFO @ Tue, 14 Jul 2020 08:29:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7262568/SRX7262568.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:29:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7262568/SRX7262568.20_summits.bed INFO @ Tue, 14 Jul 2020 08:29:40: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (229 records, 4 fields): 2 millis CompletedMACS2peakCalling