Job ID = 6626634 SRX = SRX7262569 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 101135005 spots for SRR10582196/SRR10582196.sra Written 101135005 spots for SRR10582196/SRR10582196.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626938 ("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: 00:15:42 101135005 reads; of these: 101135005 (100.00%) were unpaired; of these: 93630583 (92.58%) aligned 0 times 5525416 (5.46%) aligned exactly 1 time 1979006 (1.96%) aligned >1 times 7.42% overall alignment rate Time searching: 00:15:42 Overall time: 00:15:42 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] 1232980 / 7504422 = 0.1643 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 08:28:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7262569/SRX7262569.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7262569/SRX7262569.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7262569/SRX7262569.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7262569/SRX7262569.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 08:28:24: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:28:24: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:28:29: 1000000 INFO @ Tue, 14 Jul 2020 08:28:35: 2000000 INFO @ Tue, 14 Jul 2020 08:28:41: 3000000 INFO @ Tue, 14 Jul 2020 08:28:47: 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 08:28:53: 5000000 INFO @ Tue, 14 Jul 2020 08:28:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7262569/SRX7262569.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7262569/SRX7262569.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7262569/SRX7262569.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7262569/SRX7262569.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 08:28:54: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:28:54: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:28:59: 6000000 INFO @ Tue, 14 Jul 2020 08:29:00: 1000000 INFO @ Tue, 14 Jul 2020 08:29:00: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:29:00: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:29:00: #1 total tags in treatment: 6271442 INFO @ Tue, 14 Jul 2020 08:29:00: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:29:00: #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 08:29:00: #1 tags after filtering in treatment: 6271442 INFO @ Tue, 14 Jul 2020 08:29:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:29:00: #1 finished! INFO @ Tue, 14 Jul 2020 08:29:00: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:29:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:29:01: #2 number of paired peaks: 1410 INFO @ Tue, 14 Jul 2020 08:29:01: start model_add_line... INFO @ Tue, 14 Jul 2020 08:29:01: start X-correlation... INFO @ Tue, 14 Jul 2020 08:29:01: end of X-cor INFO @ Tue, 14 Jul 2020 08:29:01: #2 finished! INFO @ Tue, 14 Jul 2020 08:29:01: #2 predicted fragment length is 77 bps INFO @ Tue, 14 Jul 2020 08:29:01: #2 alternative fragment length(s) may be 4,77 bps INFO @ Tue, 14 Jul 2020 08:29:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7262569/SRX7262569.05_model.r WARNING @ Tue, 14 Jul 2020 08:29:01: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:29:01: #2 You may need to consider one of the other alternative d(s): 4,77 WARNING @ Tue, 14 Jul 2020 08:29:01: #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 08:29:01: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:29:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:29:06: 2000000 INFO @ Tue, 14 Jul 2020 08:29:12: 3000000 INFO @ Tue, 14 Jul 2020 08:29:14: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:29:17: 4000000 INFO @ Tue, 14 Jul 2020 08:29:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7262569/SRX7262569.05_peaks.xls INFO @ Tue, 14 Jul 2020 08:29:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7262569/SRX7262569.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:29:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7262569/SRX7262569.05_summits.bed INFO @ Tue, 14 Jul 2020 08:29:21: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1683 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 08:29:23: 5000000 INFO @ Tue, 14 Jul 2020 08:29:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7262569/SRX7262569.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7262569/SRX7262569.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7262569/SRX7262569.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7262569/SRX7262569.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 08:29:24: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:29:24: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:29:29: 6000000 INFO @ Tue, 14 Jul 2020 08:29:30: 1000000 INFO @ Tue, 14 Jul 2020 08:29:31: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:29:31: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:29:31: #1 total tags in treatment: 6271442 INFO @ Tue, 14 Jul 2020 08:29:31: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:29:31: #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 08:29:31: #1 tags after filtering in treatment: 6271442 INFO @ Tue, 14 Jul 2020 08:29:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:29:31: #1 finished! INFO @ Tue, 14 Jul 2020 08:29:31: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:29:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:29:31: #2 number of paired peaks: 1410 INFO @ Tue, 14 Jul 2020 08:29:31: start model_add_line... INFO @ Tue, 14 Jul 2020 08:29:32: start X-correlation... INFO @ Tue, 14 Jul 2020 08:29:32: end of X-cor INFO @ Tue, 14 Jul 2020 08:29:32: #2 finished! INFO @ Tue, 14 Jul 2020 08:29:32: #2 predicted fragment length is 77 bps INFO @ Tue, 14 Jul 2020 08:29:32: #2 alternative fragment length(s) may be 4,77 bps INFO @ Tue, 14 Jul 2020 08:29:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7262569/SRX7262569.10_model.r WARNING @ Tue, 14 Jul 2020 08:29:32: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:29:32: #2 You may need to consider one of the other alternative d(s): 4,77 WARNING @ Tue, 14 Jul 2020 08:29:32: #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 08:29:32: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:29:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:29:36: 2000000 INFO @ Tue, 14 Jul 2020 08:29:42: 3000000 INFO @ Tue, 14 Jul 2020 08:29:45: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:29:48: 4000000 INFO @ Tue, 14 Jul 2020 08:29:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7262569/SRX7262569.10_peaks.xls INFO @ Tue, 14 Jul 2020 08:29:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7262569/SRX7262569.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:29:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7262569/SRX7262569.10_summits.bed INFO @ Tue, 14 Jul 2020 08:29:51: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (905 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 08:29:54: 5000000 INFO @ Tue, 14 Jul 2020 08:30:00: 6000000 INFO @ Tue, 14 Jul 2020 08:30:01: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:30:01: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:30:01: #1 total tags in treatment: 6271442 INFO @ Tue, 14 Jul 2020 08:30:01: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:30:01: #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 08:30:01: #1 tags after filtering in treatment: 6271442 INFO @ Tue, 14 Jul 2020 08:30:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:30:01: #1 finished! INFO @ Tue, 14 Jul 2020 08:30:01: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:30:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:30:02: #2 number of paired peaks: 1410 INFO @ Tue, 14 Jul 2020 08:30:02: start model_add_line... INFO @ Tue, 14 Jul 2020 08:30:02: start X-correlation... INFO @ Tue, 14 Jul 2020 08:30:02: end of X-cor INFO @ Tue, 14 Jul 2020 08:30:02: #2 finished! INFO @ Tue, 14 Jul 2020 08:30:02: #2 predicted fragment length is 77 bps INFO @ Tue, 14 Jul 2020 08:30:02: #2 alternative fragment length(s) may be 4,77 bps INFO @ Tue, 14 Jul 2020 08:30:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7262569/SRX7262569.20_model.r WARNING @ Tue, 14 Jul 2020 08:30:02: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:30:02: #2 You may need to consider one of the other alternative d(s): 4,77 WARNING @ Tue, 14 Jul 2020 08:30:02: #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 08:30:02: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:30:02: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 08:30:15: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:30:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7262569/SRX7262569.20_peaks.xls INFO @ Tue, 14 Jul 2020 08:30:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7262569/SRX7262569.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:30:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7262569/SRX7262569.20_summits.bed INFO @ Tue, 14 Jul 2020 08:30:22: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (211 records, 4 fields): 2 millis CompletedMACS2peakCalling