Job ID = 14166964 SRX = SRX7723702 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 34021743 spots for SRR11084658/SRR11084658.sra Written 34021743 spots for SRR11084658/SRR11084658.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167295 ("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: 00:10:20 34021743 reads; of these: 34021743 (100.00%) were unpaired; of these: 15225434 (44.75%) aligned 0 times 14749686 (43.35%) aligned exactly 1 time 4046623 (11.89%) aligned >1 times 55.25% overall alignment rate Time searching: 00:10:20 Overall time: 00:10:20 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] 9533957 / 18796309 = 0.5072 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 08:26:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723702/SRX7723702.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723702/SRX7723702.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723702/SRX7723702.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723702/SRX7723702.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 @ Fri, 10 Dec 2021 08:26:47: #1 read tag files... INFO @ Fri, 10 Dec 2021 08:26:47: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 08:26:53: 1000000 INFO @ Fri, 10 Dec 2021 08:26:59: 2000000 INFO @ Fri, 10 Dec 2021 08:27:05: 3000000 INFO @ Fri, 10 Dec 2021 08:27:11: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 08:27:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723702/SRX7723702.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723702/SRX7723702.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723702/SRX7723702.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723702/SRX7723702.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 @ Fri, 10 Dec 2021 08:27:17: #1 read tag files... INFO @ Fri, 10 Dec 2021 08:27:17: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 08:27:18: 5000000 INFO @ Fri, 10 Dec 2021 08:27:25: 1000000 INFO @ Fri, 10 Dec 2021 08:27:25: 6000000 INFO @ Fri, 10 Dec 2021 08:27:33: 7000000 INFO @ Fri, 10 Dec 2021 08:27:33: 2000000 INFO @ Fri, 10 Dec 2021 08:27:41: 8000000 INFO @ Fri, 10 Dec 2021 08:27:41: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 08:27:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723702/SRX7723702.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723702/SRX7723702.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723702/SRX7723702.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723702/SRX7723702.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 @ Fri, 10 Dec 2021 08:27:47: #1 read tag files... INFO @ Fri, 10 Dec 2021 08:27:47: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 08:27:48: 9000000 INFO @ Fri, 10 Dec 2021 08:27:49: 4000000 INFO @ Fri, 10 Dec 2021 08:27:50: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 08:27:50: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 08:27:50: #1 total tags in treatment: 9262352 INFO @ Fri, 10 Dec 2021 08:27:50: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 08:27:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 08:27:51: #1 tags after filtering in treatment: 9262352 INFO @ Fri, 10 Dec 2021 08:27:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 08:27:51: #1 finished! INFO @ Fri, 10 Dec 2021 08:27:51: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 08:27:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 08:27:52: #2 number of paired peaks: 6693 INFO @ Fri, 10 Dec 2021 08:27:52: start model_add_line... INFO @ Fri, 10 Dec 2021 08:27:52: start X-correlation... INFO @ Fri, 10 Dec 2021 08:27:52: end of X-cor INFO @ Fri, 10 Dec 2021 08:27:52: #2 finished! INFO @ Fri, 10 Dec 2021 08:27:52: #2 predicted fragment length is 132 bps INFO @ Fri, 10 Dec 2021 08:27:52: #2 alternative fragment length(s) may be 132 bps INFO @ Fri, 10 Dec 2021 08:27:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723702/SRX7723702.05_model.r WARNING @ Fri, 10 Dec 2021 08:27:52: #2 Since the d (132) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 08:27:52: #2 You may need to consider one of the other alternative d(s): 132 WARNING @ Fri, 10 Dec 2021 08:27:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 08:27:52: #3 Call peaks... INFO @ Fri, 10 Dec 2021 08:27:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 08:27:54: 1000000 INFO @ Fri, 10 Dec 2021 08:27:56: 5000000 INFO @ Fri, 10 Dec 2021 08:28:02: 2000000 INFO @ Fri, 10 Dec 2021 08:28:04: 6000000 INFO @ Fri, 10 Dec 2021 08:28:09: 3000000 INFO @ Fri, 10 Dec 2021 08:28:11: 7000000 INFO @ Fri, 10 Dec 2021 08:28:12: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 08:28:17: 4000000 INFO @ Fri, 10 Dec 2021 08:28:19: 8000000 INFO @ Fri, 10 Dec 2021 08:28:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723702/SRX7723702.05_peaks.xls INFO @ Fri, 10 Dec 2021 08:28:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723702/SRX7723702.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 08:28:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723702/SRX7723702.05_summits.bed INFO @ Fri, 10 Dec 2021 08:28:22: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9514 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 08:28:24: 5000000 INFO @ Fri, 10 Dec 2021 08:28:26: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 08:28:28: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 08:28:28: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 08:28:28: #1 total tags in treatment: 9262352 INFO @ Fri, 10 Dec 2021 08:28:28: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 08:28:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 08:28:28: #1 tags after filtering in treatment: 9262352 INFO @ Fri, 10 Dec 2021 08:28:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 08:28:28: #1 finished! INFO @ Fri, 10 Dec 2021 08:28:28: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 08:28:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 08:28:29: #2 number of paired peaks: 6693 INFO @ Fri, 10 Dec 2021 08:28:29: start model_add_line... INFO @ Fri, 10 Dec 2021 08:28:29: start X-correlation... INFO @ Fri, 10 Dec 2021 08:28:29: end of X-cor INFO @ Fri, 10 Dec 2021 08:28:29: #2 finished! INFO @ Fri, 10 Dec 2021 08:28:29: #2 predicted fragment length is 132 bps INFO @ Fri, 10 Dec 2021 08:28:29: #2 alternative fragment length(s) may be 132 bps INFO @ Fri, 10 Dec 2021 08:28:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723702/SRX7723702.10_model.r WARNING @ Fri, 10 Dec 2021 08:28:29: #2 Since the d (132) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 08:28:29: #2 You may need to consider one of the other alternative d(s): 132 WARNING @ Fri, 10 Dec 2021 08:28:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 08:28:29: #3 Call peaks... INFO @ Fri, 10 Dec 2021 08:28:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 08:28:31: 6000000 INFO @ Fri, 10 Dec 2021 08:28:38: 7000000 INFO @ Fri, 10 Dec 2021 08:28:44: 8000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 08:28:49: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 08:28:50: 9000000 INFO @ Fri, 10 Dec 2021 08:28:52: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 08:28:52: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 08:28:52: #1 total tags in treatment: 9262352 INFO @ Fri, 10 Dec 2021 08:28:52: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 08:28:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 08:28:52: #1 tags after filtering in treatment: 9262352 INFO @ Fri, 10 Dec 2021 08:28:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 08:28:52: #1 finished! INFO @ Fri, 10 Dec 2021 08:28:52: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 08:28:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 08:28:53: #2 number of paired peaks: 6693 INFO @ Fri, 10 Dec 2021 08:28:53: start model_add_line... INFO @ Fri, 10 Dec 2021 08:28:53: start X-correlation... INFO @ Fri, 10 Dec 2021 08:28:53: end of X-cor INFO @ Fri, 10 Dec 2021 08:28:53: #2 finished! INFO @ Fri, 10 Dec 2021 08:28:53: #2 predicted fragment length is 132 bps INFO @ Fri, 10 Dec 2021 08:28:53: #2 alternative fragment length(s) may be 132 bps INFO @ Fri, 10 Dec 2021 08:28:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723702/SRX7723702.20_model.r WARNING @ Fri, 10 Dec 2021 08:28:53: #2 Since the d (132) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 08:28:53: #2 You may need to consider one of the other alternative d(s): 132 WARNING @ Fri, 10 Dec 2021 08:28:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 08:28:53: #3 Call peaks... INFO @ Fri, 10 Dec 2021 08:28:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 08:28:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723702/SRX7723702.10_peaks.xls INFO @ Fri, 10 Dec 2021 08:28:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723702/SRX7723702.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 08:29:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723702/SRX7723702.10_summits.bed INFO @ Fri, 10 Dec 2021 08:29:00: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (6992 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 08:29:13: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 08:29:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723702/SRX7723702.20_peaks.xls INFO @ Fri, 10 Dec 2021 08:29:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723702/SRX7723702.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 08:29:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723702/SRX7723702.20_summits.bed INFO @ Fri, 10 Dec 2021 08:29:23: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (4414 records, 4 fields): 5 millis CompletedMACS2peakCalling