Job ID = 12264887 SRX = SRX3032285 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 9587034 spots for SRR5863975/SRR5863975.sra Written 9587034 spots for SRR5863975/SRR5863975.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265032 ("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: 00:02:46 9587034 reads; of these: 9587034 (100.00%) were unpaired; of these: 1327578 (13.85%) aligned 0 times 7224714 (75.36%) aligned exactly 1 time 1034742 (10.79%) aligned >1 times 86.15% overall alignment rate Time searching: 00:02:46 Overall time: 00:02:46 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_rmdupse_core] 2415139 / 8259456 = 0.2924 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 05:59:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032285/SRX3032285.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032285/SRX3032285.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032285/SRX3032285.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032285/SRX3032285.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 05:59:58: #1 read tag files... INFO @ Sat, 03 Apr 2021 05:59:58: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:00:07: 1000000 INFO @ Sat, 03 Apr 2021 06:00:16: 2000000 INFO @ Sat, 03 Apr 2021 06:00:24: 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 06:00:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032285/SRX3032285.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032285/SRX3032285.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032285/SRX3032285.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032285/SRX3032285.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 06:00:28: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:00:28: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:00:33: 4000000 INFO @ Sat, 03 Apr 2021 06:00:38: 1000000 INFO @ Sat, 03 Apr 2021 06:00:42: 5000000 INFO @ Sat, 03 Apr 2021 06:00:47: 2000000 INFO @ Sat, 03 Apr 2021 06:00:49: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 06:00:49: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 06:00:49: #1 total tags in treatment: 5844317 INFO @ Sat, 03 Apr 2021 06:00:49: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:00:49: #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 06:00:49: #1 tags after filtering in treatment: 5844317 INFO @ Sat, 03 Apr 2021 06:00:49: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:00:49: #1 finished! INFO @ Sat, 03 Apr 2021 06:00:49: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:00:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:00:50: #2 number of paired peaks: 4104 INFO @ Sat, 03 Apr 2021 06:00:50: start model_add_line... INFO @ Sat, 03 Apr 2021 06:00:50: start X-correlation... INFO @ Sat, 03 Apr 2021 06:00:50: end of X-cor INFO @ Sat, 03 Apr 2021 06:00:50: #2 finished! INFO @ Sat, 03 Apr 2021 06:00:50: #2 predicted fragment length is 96 bps INFO @ Sat, 03 Apr 2021 06:00:50: #2 alternative fragment length(s) may be 96 bps INFO @ Sat, 03 Apr 2021 06:00:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032285/SRX3032285.05_model.r WARNING @ Sat, 03 Apr 2021 06:00:50: #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 06:00:50: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Sat, 03 Apr 2021 06:00:50: #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 06:00:50: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:00:50: #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 06:00:56: 3000000 INFO @ Sat, 03 Apr 2021 06:00:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032285/SRX3032285.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032285/SRX3032285.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032285/SRX3032285.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032285/SRX3032285.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 06:00:58: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:00:58: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:01:05: 4000000 INFO @ Sat, 03 Apr 2021 06:01:06: 1000000 INFO @ Sat, 03 Apr 2021 06:01:08: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:01:14: 2000000 INFO @ Sat, 03 Apr 2021 06:01:14: 5000000 INFO @ Sat, 03 Apr 2021 06:01:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032285/SRX3032285.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:01:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032285/SRX3032285.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:01:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032285/SRX3032285.05_summits.bed INFO @ Sat, 03 Apr 2021 06:01:19: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (15614 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:01:21: 3000000 INFO @ Sat, 03 Apr 2021 06:01:22: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 06:01:22: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 06:01:22: #1 total tags in treatment: 5844317 INFO @ Sat, 03 Apr 2021 06:01:22: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:01:22: #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 06:01:22: #1 tags after filtering in treatment: 5844317 INFO @ Sat, 03 Apr 2021 06:01:22: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:01:22: #1 finished! INFO @ Sat, 03 Apr 2021 06:01:22: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:01:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:01:23: #2 number of paired peaks: 4104 INFO @ Sat, 03 Apr 2021 06:01:23: start model_add_line... INFO @ Sat, 03 Apr 2021 06:01:23: start X-correlation... INFO @ Sat, 03 Apr 2021 06:01:23: end of X-cor INFO @ Sat, 03 Apr 2021 06:01:23: #2 finished! INFO @ Sat, 03 Apr 2021 06:01:23: #2 predicted fragment length is 96 bps INFO @ Sat, 03 Apr 2021 06:01:23: #2 alternative fragment length(s) may be 96 bps INFO @ Sat, 03 Apr 2021 06:01:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032285/SRX3032285.10_model.r WARNING @ Sat, 03 Apr 2021 06:01:23: #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 06:01:23: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Sat, 03 Apr 2021 06:01:23: #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 06:01:23: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:01:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:01:29: 4000000 INFO @ Sat, 03 Apr 2021 06:01:36: 5000000 INFO @ Sat, 03 Apr 2021 06:01:41: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:01:43: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 06:01:43: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 06:01:43: #1 total tags in treatment: 5844317 INFO @ Sat, 03 Apr 2021 06:01:43: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:01:43: #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 06:01:43: #1 tags after filtering in treatment: 5844317 INFO @ Sat, 03 Apr 2021 06:01:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:01:43: #1 finished! INFO @ Sat, 03 Apr 2021 06:01:43: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:01:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:01:44: #2 number of paired peaks: 4104 INFO @ Sat, 03 Apr 2021 06:01:44: start model_add_line... INFO @ Sat, 03 Apr 2021 06:01:44: start X-correlation... INFO @ Sat, 03 Apr 2021 06:01:44: end of X-cor INFO @ Sat, 03 Apr 2021 06:01:44: #2 finished! INFO @ Sat, 03 Apr 2021 06:01:44: #2 predicted fragment length is 96 bps INFO @ Sat, 03 Apr 2021 06:01:44: #2 alternative fragment length(s) may be 96 bps INFO @ Sat, 03 Apr 2021 06:01:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032285/SRX3032285.20_model.r WARNING @ Sat, 03 Apr 2021 06:01:44: #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 06:01:44: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Sat, 03 Apr 2021 06:01:44: #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 06:01:44: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:01:44: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:01:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032285/SRX3032285.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:01:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032285/SRX3032285.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:01:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032285/SRX3032285.10_summits.bed INFO @ Sat, 03 Apr 2021 06:01:51: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (8836 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:02:02: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:02:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032285/SRX3032285.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:02:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032285/SRX3032285.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:02:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032285/SRX3032285.20_summits.bed INFO @ Sat, 03 Apr 2021 06:02:12: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3120 records, 4 fields): 31 millis CompletedMACS2peakCalling