Job ID = 12265689 SRX = SRX7281012 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 25200642 spots for SRR10601387/SRR10601387.sra Written 25200642 spots for SRR10601387/SRR10601387.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265829 ("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: 00:08:09 25200642 reads; of these: 25200642 (100.00%) were unpaired; of these: 16670908 (66.15%) aligned 0 times 6874437 (27.28%) aligned exactly 1 time 1655297 (6.57%) aligned >1 times 33.85% overall alignment rate Time searching: 00:08:09 Overall time: 00:08:10 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] 3038449 / 8529734 = 0.3562 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 08:21:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7281012/SRX7281012.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7281012/SRX7281012.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7281012/SRX7281012.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7281012/SRX7281012.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, 03 Apr 2021 08:21:54: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:21:54: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:22:01: 1000000 INFO @ Sat, 03 Apr 2021 08:22:08: 2000000 INFO @ Sat, 03 Apr 2021 08:22:15: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 08:22:23: 4000000 INFO @ Sat, 03 Apr 2021 08:22:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7281012/SRX7281012.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7281012/SRX7281012.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7281012/SRX7281012.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7281012/SRX7281012.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, 03 Apr 2021 08:22:24: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:22:24: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:22:30: 5000000 INFO @ Sat, 03 Apr 2021 08:22:31: 1000000 INFO @ Sat, 03 Apr 2021 08:22:33: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 08:22:33: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 08:22:33: #1 total tags in treatment: 5491285 INFO @ Sat, 03 Apr 2021 08:22:33: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:22:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 08:22:33: #1 tags after filtering in treatment: 5491285 INFO @ Sat, 03 Apr 2021 08:22:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 08:22:33: #1 finished! INFO @ Sat, 03 Apr 2021 08:22:33: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:22:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:22:34: #2 number of paired peaks: 2860 INFO @ Sat, 03 Apr 2021 08:22:34: start model_add_line... INFO @ Sat, 03 Apr 2021 08:22:34: start X-correlation... INFO @ Sat, 03 Apr 2021 08:22:34: end of X-cor INFO @ Sat, 03 Apr 2021 08:22:34: #2 finished! INFO @ Sat, 03 Apr 2021 08:22:34: #2 predicted fragment length is 96 bps INFO @ Sat, 03 Apr 2021 08:22:34: #2 alternative fragment length(s) may be 96 bps INFO @ Sat, 03 Apr 2021 08:22:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7281012/SRX7281012.05_model.r WARNING @ Sat, 03 Apr 2021 08:22:34: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:22:34: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Sat, 03 Apr 2021 08:22:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 08:22:34: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:22:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:22:38: 2000000 INFO @ Sat, 03 Apr 2021 08:22:44: 3000000 INFO @ Sat, 03 Apr 2021 08:22:45: #3 Call peaks for each chromosome... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 08:22:51: 4000000 INFO @ Sat, 03 Apr 2021 08:22:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7281012/SRX7281012.05_peaks.xls INFO @ Sat, 03 Apr 2021 08:22:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7281012/SRX7281012.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:22:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7281012/SRX7281012.05_summits.bed INFO @ Sat, 03 Apr 2021 08:22:52: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (12146 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:22:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7281012/SRX7281012.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7281012/SRX7281012.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7281012/SRX7281012.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7281012/SRX7281012.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, 03 Apr 2021 08:22:53: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:22:53: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:22:58: 5000000 INFO @ Sat, 03 Apr 2021 08:23:00: 1000000 INFO @ Sat, 03 Apr 2021 08:23:01: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 08:23:01: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 08:23:01: #1 total tags in treatment: 5491285 INFO @ Sat, 03 Apr 2021 08:23:01: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:23:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 08:23:01: #1 tags after filtering in treatment: 5491285 INFO @ Sat, 03 Apr 2021 08:23:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 08:23:01: #1 finished! INFO @ Sat, 03 Apr 2021 08:23:01: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:23:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:23:02: #2 number of paired peaks: 2860 INFO @ Sat, 03 Apr 2021 08:23:02: start model_add_line... INFO @ Sat, 03 Apr 2021 08:23:02: start X-correlation... INFO @ Sat, 03 Apr 2021 08:23:02: end of X-cor INFO @ Sat, 03 Apr 2021 08:23:02: #2 finished! INFO @ Sat, 03 Apr 2021 08:23:02: #2 predicted fragment length is 96 bps INFO @ Sat, 03 Apr 2021 08:23:02: #2 alternative fragment length(s) may be 96 bps INFO @ Sat, 03 Apr 2021 08:23:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7281012/SRX7281012.10_model.r WARNING @ Sat, 03 Apr 2021 08:23:02: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:23:02: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Sat, 03 Apr 2021 08:23:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 08:23:02: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:23:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:23:06: 2000000 INFO @ Sat, 03 Apr 2021 08:23:13: 3000000 INFO @ Sat, 03 Apr 2021 08:23:13: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:23:19: 4000000 INFO @ Sat, 03 Apr 2021 08:23:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7281012/SRX7281012.10_peaks.xls INFO @ Sat, 03 Apr 2021 08:23:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7281012/SRX7281012.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:23:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7281012/SRX7281012.10_summits.bed INFO @ Sat, 03 Apr 2021 08:23:20: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (7137 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:23:25: 5000000 INFO @ Sat, 03 Apr 2021 08:23:28: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 08:23:28: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 08:23:28: #1 total tags in treatment: 5491285 INFO @ Sat, 03 Apr 2021 08:23:28: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:23:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 08:23:28: #1 tags after filtering in treatment: 5491285 INFO @ Sat, 03 Apr 2021 08:23:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 08:23:28: #1 finished! INFO @ Sat, 03 Apr 2021 08:23:28: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:23:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:23:29: #2 number of paired peaks: 2860 INFO @ Sat, 03 Apr 2021 08:23:29: start model_add_line... BedGraph に変換しました。 INFO @ Sat, 03 Apr 2021 08:23:29: start X-correlation... BigWig に変換中... INFO @ Sat, 03 Apr 2021 08:23:29: end of X-cor INFO @ Sat, 03 Apr 2021 08:23:29: #2 finished! INFO @ Sat, 03 Apr 2021 08:23:29: #2 predicted fragment length is 96 bps INFO @ Sat, 03 Apr 2021 08:23:29: #2 alternative fragment length(s) may be 96 bps INFO @ Sat, 03 Apr 2021 08:23:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7281012/SRX7281012.20_model.r WARNING @ Sat, 03 Apr 2021 08:23:29: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:23:29: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Sat, 03 Apr 2021 08:23:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 08:23:29: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:23:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:23:40: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 08:23:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7281012/SRX7281012.20_peaks.xls INFO @ Sat, 03 Apr 2021 08:23:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7281012/SRX7281012.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:23:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7281012/SRX7281012.20_summits.bed INFO @ Sat, 03 Apr 2021 08:23:46: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2806 records, 4 fields): 7 millis CompletedMACS2peakCalling