Job ID = 6626635 SRX = SRX7262570 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 104445940 spots for SRR10582197/SRR10582197.sra Written 104445940 spots for SRR10582197/SRR10582197.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626969 ("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: 00:18:45 104445940 reads; of these: 104445940 (100.00%) were unpaired; of these: 86510821 (82.83%) aligned 0 times 13946622 (13.35%) aligned exactly 1 time 3988497 (3.82%) aligned >1 times 17.17% overall alignment rate Time searching: 00:18:46 Overall time: 00:18:46 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_sort_core] merging from 8 files... [bam_rmdupse_core] 6364659 / 17935119 = 0.3549 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 08:34:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7262570/SRX7262570.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7262570/SRX7262570.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7262570/SRX7262570.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7262570/SRX7262570.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 08:34:51: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:34:51: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:35:01: 1000000 INFO @ Tue, 14 Jul 2020 08:35:10: 2000000 INFO @ Tue, 14 Jul 2020 08:35:19: 3000000 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 08:35:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7262570/SRX7262570.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7262570/SRX7262570.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7262570/SRX7262570.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7262570/SRX7262570.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 08:35:21: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:35:21: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:35:27: 1000000 INFO @ Tue, 14 Jul 2020 08:35:28: 4000000 INFO @ Tue, 14 Jul 2020 08:35:34: 2000000 INFO @ Tue, 14 Jul 2020 08:35:38: 5000000 INFO @ Tue, 14 Jul 2020 08:35:40: 3000000 INFO @ Tue, 14 Jul 2020 08:35:46: 4000000 INFO @ Tue, 14 Jul 2020 08:35:48: 6000000 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 08:35:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7262570/SRX7262570.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7262570/SRX7262570.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7262570/SRX7262570.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7262570/SRX7262570.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 08:35:51: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:35:51: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:35:53: 5000000 INFO @ Tue, 14 Jul 2020 08:35:57: 7000000 INFO @ Tue, 14 Jul 2020 08:35:57: 1000000 INFO @ Tue, 14 Jul 2020 08:35:59: 6000000 INFO @ Tue, 14 Jul 2020 08:36:04: 2000000 INFO @ Tue, 14 Jul 2020 08:36:06: 7000000 INFO @ Tue, 14 Jul 2020 08:36:06: 8000000 INFO @ Tue, 14 Jul 2020 08:36:11: 3000000 INFO @ Tue, 14 Jul 2020 08:36:13: 8000000 INFO @ Tue, 14 Jul 2020 08:36:15: 9000000 INFO @ Tue, 14 Jul 2020 08:36:17: 4000000 INFO @ Tue, 14 Jul 2020 08:36:19: 9000000 INFO @ Tue, 14 Jul 2020 08:36:24: 5000000 INFO @ Tue, 14 Jul 2020 08:36:24: 10000000 INFO @ Tue, 14 Jul 2020 08:36:26: 10000000 INFO @ Tue, 14 Jul 2020 08:36:30: 6000000 INFO @ Tue, 14 Jul 2020 08:36:33: 11000000 INFO @ Tue, 14 Jul 2020 08:36:34: 11000000 INFO @ Tue, 14 Jul 2020 08:36:36: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:36:36: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:36:36: #1 total tags in treatment: 11570460 INFO @ Tue, 14 Jul 2020 08:36:36: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:36:36: #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 08:36:37: #1 tags after filtering in treatment: 11570460 INFO @ Tue, 14 Jul 2020 08:36:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:36:37: #1 finished! INFO @ Tue, 14 Jul 2020 08:36:37: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:36:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:36:37: 7000000 INFO @ Tue, 14 Jul 2020 08:36:38: #2 number of paired peaks: 9065 INFO @ Tue, 14 Jul 2020 08:36:38: start model_add_line... INFO @ Tue, 14 Jul 2020 08:36:38: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:36:38: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:36:38: #1 total tags in treatment: 11570460 INFO @ Tue, 14 Jul 2020 08:36:38: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:36:38: #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 08:36:38: start X-correlation... INFO @ Tue, 14 Jul 2020 08:36:38: #1 tags after filtering in treatment: 11570460 INFO @ Tue, 14 Jul 2020 08:36:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:36:38: #1 finished! INFO @ Tue, 14 Jul 2020 08:36:38: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:36:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:36:38: end of X-cor INFO @ Tue, 14 Jul 2020 08:36:38: #2 finished! INFO @ Tue, 14 Jul 2020 08:36:38: #2 predicted fragment length is 131 bps INFO @ Tue, 14 Jul 2020 08:36:38: #2 alternative fragment length(s) may be 131 bps INFO @ Tue, 14 Jul 2020 08:36:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7262570/SRX7262570.10_model.r WARNING @ Tue, 14 Jul 2020 08:36:38: #2 Since the d (131) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:36:38: #2 You may need to consider one of the other alternative d(s): 131 WARNING @ Tue, 14 Jul 2020 08:36:38: #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 08:36:38: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:36:38: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 08:36:40: #2 number of paired peaks: 9065 INFO @ Tue, 14 Jul 2020 08:36:40: start model_add_line... INFO @ Tue, 14 Jul 2020 08:36:40: start X-correlation... INFO @ Tue, 14 Jul 2020 08:36:40: end of X-cor INFO @ Tue, 14 Jul 2020 08:36:40: #2 finished! INFO @ Tue, 14 Jul 2020 08:36:40: #2 predicted fragment length is 131 bps INFO @ Tue, 14 Jul 2020 08:36:40: #2 alternative fragment length(s) may be 131 bps INFO @ Tue, 14 Jul 2020 08:36:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7262570/SRX7262570.05_model.r WARNING @ Tue, 14 Jul 2020 08:36:40: #2 Since the d (131) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:36:40: #2 You may need to consider one of the other alternative d(s): 131 WARNING @ Tue, 14 Jul 2020 08:36:40: #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 08:36:40: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:36:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:36:43: 8000000 INFO @ Tue, 14 Jul 2020 08:36:49: 9000000 INFO @ Tue, 14 Jul 2020 08:36:56: 10000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 08:37:02: 11000000 INFO @ Tue, 14 Jul 2020 08:37:05: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:37:05: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:37:05: #1 total tags in treatment: 11570460 INFO @ Tue, 14 Jul 2020 08:37:05: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:37:05: #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 08:37:05: #1 tags after filtering in treatment: 11570460 INFO @ Tue, 14 Jul 2020 08:37:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:37:05: #1 finished! INFO @ Tue, 14 Jul 2020 08:37:05: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:37:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:37:07: #2 number of paired peaks: 9065 INFO @ Tue, 14 Jul 2020 08:37:07: start model_add_line... INFO @ Tue, 14 Jul 2020 08:37:07: start X-correlation... INFO @ Tue, 14 Jul 2020 08:37:07: end of X-cor INFO @ Tue, 14 Jul 2020 08:37:07: #2 finished! INFO @ Tue, 14 Jul 2020 08:37:07: #2 predicted fragment length is 131 bps INFO @ Tue, 14 Jul 2020 08:37:07: #2 alternative fragment length(s) may be 131 bps INFO @ Tue, 14 Jul 2020 08:37:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7262570/SRX7262570.20_model.r WARNING @ Tue, 14 Jul 2020 08:37:07: #2 Since the d (131) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:37:07: #2 You may need to consider one of the other alternative d(s): 131 WARNING @ Tue, 14 Jul 2020 08:37:07: #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 08:37:07: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:37:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:37:07: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:37:10: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:37:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7262570/SRX7262570.10_peaks.xls INFO @ Tue, 14 Jul 2020 08:37:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7262570/SRX7262570.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:37:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7262570/SRX7262570.10_summits.bed INFO @ Tue, 14 Jul 2020 08:37:20: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (7300 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:37:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7262570/SRX7262570.05_peaks.xls INFO @ Tue, 14 Jul 2020 08:37:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7262570/SRX7262570.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:37:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7262570/SRX7262570.05_summits.bed INFO @ Tue, 14 Jul 2020 08:37:24: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9879 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:37:35: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:37:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7262570/SRX7262570.20_peaks.xls INFO @ Tue, 14 Jul 2020 08:37:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7262570/SRX7262570.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:37:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7262570/SRX7262570.20_summits.bed INFO @ Tue, 14 Jul 2020 08:37:47: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4601 records, 4 fields): 6 millis CompletedMACS2peakCalling