Job ID = 12265703 SRX = SRX7281019 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 11486369 spots for SRR10601367/SRR10601367.sra Written 11486369 spots for SRR10601367/SRR10601367.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265849 ("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: 00:03:18 11486369 reads; of these: 11486369 (100.00%) were unpaired; of these: 7192672 (62.62%) aligned 0 times 3550823 (30.91%) aligned exactly 1 time 742874 (6.47%) aligned >1 times 37.38% overall alignment rate Time searching: 00:03:18 Overall time: 00:03:18 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] 1144864 / 4293697 = 0.2666 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 08:22:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7281019/SRX7281019.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7281019/SRX7281019.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7281019/SRX7281019.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7281019/SRX7281019.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 08:22:27: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:22:27: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:22:34: 1000000 INFO @ Sat, 03 Apr 2021 08:22:41: 2000000 INFO @ Sat, 03 Apr 2021 08:22:47: 3000000 INFO @ Sat, 03 Apr 2021 08:22:48: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 08:22:48: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 08:22:48: #1 total tags in treatment: 3148833 INFO @ Sat, 03 Apr 2021 08:22:48: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:22:48: #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 08:22:48: #1 tags after filtering in treatment: 3148833 INFO @ Sat, 03 Apr 2021 08:22:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 08:22:48: #1 finished! INFO @ Sat, 03 Apr 2021 08:22:48: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:22:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:22:49: #2 number of paired peaks: 4464 INFO @ Sat, 03 Apr 2021 08:22:49: start model_add_line... INFO @ Sat, 03 Apr 2021 08:22:49: start X-correlation... INFO @ Sat, 03 Apr 2021 08:22:49: end of X-cor INFO @ Sat, 03 Apr 2021 08:22:49: #2 finished! INFO @ Sat, 03 Apr 2021 08:22:49: #2 predicted fragment length is 95 bps INFO @ Sat, 03 Apr 2021 08:22:49: #2 alternative fragment length(s) may be 95 bps INFO @ Sat, 03 Apr 2021 08:22:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7281019/SRX7281019.05_model.r WARNING @ Sat, 03 Apr 2021 08:22:49: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:22:49: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Sat, 03 Apr 2021 08:22:49: #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 08:22:49: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:22:49: #3 Pre-compute pvalue-qvalue table... 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 08:22:56: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:22:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7281019/SRX7281019.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7281019/SRX7281019.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7281019/SRX7281019.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7281019/SRX7281019.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 08:22:57: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:22:57: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:23:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7281019/SRX7281019.05_peaks.xls INFO @ Sat, 03 Apr 2021 08:23:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7281019/SRX7281019.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:23:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7281019/SRX7281019.05_summits.bed INFO @ Sat, 03 Apr 2021 08:23:00: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10637 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:23:04: 1000000 INFO @ Sat, 03 Apr 2021 08:23:11: 2000000 INFO @ Sat, 03 Apr 2021 08:23:17: 3000000 INFO @ Sat, 03 Apr 2021 08:23:18: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 08:23:18: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 08:23:18: #1 total tags in treatment: 3148833 INFO @ Sat, 03 Apr 2021 08:23:18: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:23:18: #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 08:23:18: #1 tags after filtering in treatment: 3148833 INFO @ Sat, 03 Apr 2021 08:23:18: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 08:23:18: #1 finished! INFO @ Sat, 03 Apr 2021 08:23:18: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:23:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:23:19: #2 number of paired peaks: 4464 INFO @ Sat, 03 Apr 2021 08:23:19: start model_add_line... INFO @ Sat, 03 Apr 2021 08:23:19: start X-correlation... INFO @ Sat, 03 Apr 2021 08:23:19: end of X-cor INFO @ Sat, 03 Apr 2021 08:23:19: #2 finished! INFO @ Sat, 03 Apr 2021 08:23:19: #2 predicted fragment length is 95 bps INFO @ Sat, 03 Apr 2021 08:23:19: #2 alternative fragment length(s) may be 95 bps INFO @ Sat, 03 Apr 2021 08:23:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7281019/SRX7281019.10_model.r WARNING @ Sat, 03 Apr 2021 08:23:19: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:23:19: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Sat, 03 Apr 2021 08:23:19: #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 08:23:19: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:23:19: #3 Pre-compute pvalue-qvalue table... 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 08:23:26: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:23:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7281019/SRX7281019.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7281019/SRX7281019.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7281019/SRX7281019.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7281019/SRX7281019.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 08:23:27: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:23:27: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:23:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7281019/SRX7281019.10_peaks.xls INFO @ Sat, 03 Apr 2021 08:23:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7281019/SRX7281019.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:23:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7281019/SRX7281019.10_summits.bed INFO @ Sat, 03 Apr 2021 08:23:30: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5851 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:23:36: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 08:23:44: 2000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 08:23:53: 3000000 INFO @ Sat, 03 Apr 2021 08:23:54: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 08:23:54: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 08:23:54: #1 total tags in treatment: 3148833 INFO @ Sat, 03 Apr 2021 08:23:54: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:23:54: #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 08:23:54: #1 tags after filtering in treatment: 3148833 INFO @ Sat, 03 Apr 2021 08:23:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 08:23:54: #1 finished! INFO @ Sat, 03 Apr 2021 08:23:54: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:23:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:23:55: #2 number of paired peaks: 4464 INFO @ Sat, 03 Apr 2021 08:23:55: start model_add_line... INFO @ Sat, 03 Apr 2021 08:23:55: start X-correlation... INFO @ Sat, 03 Apr 2021 08:23:55: end of X-cor INFO @ Sat, 03 Apr 2021 08:23:55: #2 finished! INFO @ Sat, 03 Apr 2021 08:23:55: #2 predicted fragment length is 95 bps INFO @ Sat, 03 Apr 2021 08:23:55: #2 alternative fragment length(s) may be 95 bps INFO @ Sat, 03 Apr 2021 08:23:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7281019/SRX7281019.20_model.r WARNING @ Sat, 03 Apr 2021 08:23:55: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:23:55: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Sat, 03 Apr 2021 08:23:55: #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 08:23:55: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:23:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:24:02: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:24:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7281019/SRX7281019.20_peaks.xls INFO @ Sat, 03 Apr 2021 08:24:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7281019/SRX7281019.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:24:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7281019/SRX7281019.20_summits.bed INFO @ Sat, 03 Apr 2021 08:24:06: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (2024 records, 4 fields): 4 millis CompletedMACS2peakCalling