Job ID = 6529446 SRX = SRX2870713 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:20:59 48806510 reads; of these: 48806510 (100.00%) were unpaired; of these: 1993491 (4.08%) aligned 0 times 33415771 (68.47%) aligned exactly 1 time 13397248 (27.45%) aligned >1 times 95.92% overall alignment rate Time searching: 00:20:59 Overall time: 00:20:59 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 20 files... [bam_rmdupse_core] 26684398 / 46813019 = 0.5700 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, 30 Jun 2020 02:17:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2870713/SRX2870713.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2870713/SRX2870713.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2870713/SRX2870713.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2870713/SRX2870713.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, 30 Jun 2020 02:17:29: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:17:29: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:17:36: 1000000 INFO @ Tue, 30 Jun 2020 02:17:44: 2000000 INFO @ Tue, 30 Jun 2020 02:17:51: 3000000 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, 30 Jun 2020 02:17:59: 4000000 INFO @ Tue, 30 Jun 2020 02:17:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2870713/SRX2870713.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2870713/SRX2870713.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2870713/SRX2870713.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2870713/SRX2870713.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, 30 Jun 2020 02:17:59: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:17:59: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:18:07: 5000000 INFO @ Tue, 30 Jun 2020 02:18:07: 1000000 INFO @ Tue, 30 Jun 2020 02:18:15: 6000000 INFO @ Tue, 30 Jun 2020 02:18:16: 2000000 INFO @ Tue, 30 Jun 2020 02:18:23: 7000000 INFO @ Tue, 30 Jun 2020 02:18:24: 3000000 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, 30 Jun 2020 02:18:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2870713/SRX2870713.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2870713/SRX2870713.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2870713/SRX2870713.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2870713/SRX2870713.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, 30 Jun 2020 02:18:29: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:18:29: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:18:31: 8000000 INFO @ Tue, 30 Jun 2020 02:18:33: 4000000 INFO @ Tue, 30 Jun 2020 02:18:38: 1000000 INFO @ Tue, 30 Jun 2020 02:18:39: 9000000 INFO @ Tue, 30 Jun 2020 02:18:42: 5000000 INFO @ Tue, 30 Jun 2020 02:18:47: 10000000 INFO @ Tue, 30 Jun 2020 02:18:47: 2000000 INFO @ Tue, 30 Jun 2020 02:18:51: 6000000 INFO @ Tue, 30 Jun 2020 02:18:55: 11000000 INFO @ Tue, 30 Jun 2020 02:18:56: 3000000 INFO @ Tue, 30 Jun 2020 02:19:00: 7000000 INFO @ Tue, 30 Jun 2020 02:19:03: 12000000 INFO @ Tue, 30 Jun 2020 02:19:05: 4000000 INFO @ Tue, 30 Jun 2020 02:19:08: 8000000 INFO @ Tue, 30 Jun 2020 02:19:11: 13000000 INFO @ Tue, 30 Jun 2020 02:19:14: 5000000 INFO @ Tue, 30 Jun 2020 02:19:17: 9000000 INFO @ Tue, 30 Jun 2020 02:19:19: 14000000 INFO @ Tue, 30 Jun 2020 02:19:23: 6000000 INFO @ Tue, 30 Jun 2020 02:19:26: 10000000 INFO @ Tue, 30 Jun 2020 02:19:27: 15000000 INFO @ Tue, 30 Jun 2020 02:19:32: 7000000 INFO @ Tue, 30 Jun 2020 02:19:35: 11000000 INFO @ Tue, 30 Jun 2020 02:19:36: 16000000 INFO @ Tue, 30 Jun 2020 02:19:40: 8000000 INFO @ Tue, 30 Jun 2020 02:19:43: 12000000 INFO @ Tue, 30 Jun 2020 02:19:44: 17000000 INFO @ Tue, 30 Jun 2020 02:19:49: 9000000 INFO @ Tue, 30 Jun 2020 02:19:52: 18000000 INFO @ Tue, 30 Jun 2020 02:19:52: 13000000 INFO @ Tue, 30 Jun 2020 02:19:58: 10000000 INFO @ Tue, 30 Jun 2020 02:20:00: 19000000 INFO @ Tue, 30 Jun 2020 02:20:01: 14000000 INFO @ Tue, 30 Jun 2020 02:20:07: 11000000 INFO @ Tue, 30 Jun 2020 02:20:08: 20000000 INFO @ Tue, 30 Jun 2020 02:20:10: #1 tag size is determined as 75 bps INFO @ Tue, 30 Jun 2020 02:20:10: #1 tag size = 75 INFO @ Tue, 30 Jun 2020 02:20:10: #1 total tags in treatment: 20128621 INFO @ Tue, 30 Jun 2020 02:20:10: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:20:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:20:10: 15000000 INFO @ Tue, 30 Jun 2020 02:20:10: #1 tags after filtering in treatment: 20128587 INFO @ Tue, 30 Jun 2020 02:20:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:20:10: #1 finished! INFO @ Tue, 30 Jun 2020 02:20:10: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:20:10: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:20:12: #2 number of paired peaks: 1131 INFO @ Tue, 30 Jun 2020 02:20:12: start model_add_line... INFO @ Tue, 30 Jun 2020 02:20:12: start X-correlation... INFO @ Tue, 30 Jun 2020 02:20:12: end of X-cor INFO @ Tue, 30 Jun 2020 02:20:12: #2 finished! INFO @ Tue, 30 Jun 2020 02:20:12: #2 predicted fragment length is 74 bps INFO @ Tue, 30 Jun 2020 02:20:12: #2 alternative fragment length(s) may be 3,74 bps INFO @ Tue, 30 Jun 2020 02:20:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2870713/SRX2870713.05_model.r WARNING @ Tue, 30 Jun 2020 02:20:12: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:20:12: #2 You may need to consider one of the other alternative d(s): 3,74 WARNING @ Tue, 30 Jun 2020 02:20:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:20:12: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:20:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:20:15: 12000000 INFO @ Tue, 30 Jun 2020 02:20:19: 16000000 INFO @ Tue, 30 Jun 2020 02:20:24: 13000000 INFO @ Tue, 30 Jun 2020 02:20:28: 17000000 INFO @ Tue, 30 Jun 2020 02:20:33: 14000000 INFO @ Tue, 30 Jun 2020 02:20:36: 18000000 INFO @ Tue, 30 Jun 2020 02:20:41: 15000000 INFO @ Tue, 30 Jun 2020 02:20:45: 19000000 INFO @ Tue, 30 Jun 2020 02:20:51: 16000000 INFO @ Tue, 30 Jun 2020 02:20:54: 20000000 INFO @ Tue, 30 Jun 2020 02:20:54: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:20:55: #1 tag size is determined as 75 bps INFO @ Tue, 30 Jun 2020 02:20:55: #1 tag size = 75 INFO @ Tue, 30 Jun 2020 02:20:55: #1 total tags in treatment: 20128621 INFO @ Tue, 30 Jun 2020 02:20:55: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:20:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:20:56: #1 tags after filtering in treatment: 20128587 INFO @ Tue, 30 Jun 2020 02:20:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:20:56: #1 finished! INFO @ Tue, 30 Jun 2020 02:20:56: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:20:56: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:20:57: #2 number of paired peaks: 1131 INFO @ Tue, 30 Jun 2020 02:20:57: start model_add_line... INFO @ Tue, 30 Jun 2020 02:20:57: start X-correlation... INFO @ Tue, 30 Jun 2020 02:20:57: end of X-cor INFO @ Tue, 30 Jun 2020 02:20:57: #2 finished! INFO @ Tue, 30 Jun 2020 02:20:57: #2 predicted fragment length is 74 bps INFO @ Tue, 30 Jun 2020 02:20:57: #2 alternative fragment length(s) may be 3,74 bps INFO @ Tue, 30 Jun 2020 02:20:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2870713/SRX2870713.10_model.r WARNING @ Tue, 30 Jun 2020 02:20:57: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:20:57: #2 You may need to consider one of the other alternative d(s): 3,74 WARNING @ Tue, 30 Jun 2020 02:20:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:20:57: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:20:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:20:59: 17000000 INFO @ Tue, 30 Jun 2020 02:21:07: 18000000 INFO @ Tue, 30 Jun 2020 02:21:15: 19000000 INFO @ Tue, 30 Jun 2020 02:21:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2870713/SRX2870713.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:21:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2870713/SRX2870713.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:21:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2870713/SRX2870713.05_summits.bed INFO @ Tue, 30 Jun 2020 02:21:15: Done! pass1 - making usageList (845 chroms): 2 millis pass2 - checking and writing primary data (3967 records, 4 fields): 41 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:21:23: 20000000 INFO @ Tue, 30 Jun 2020 02:21:24: #1 tag size is determined as 75 bps INFO @ Tue, 30 Jun 2020 02:21:24: #1 tag size = 75 INFO @ Tue, 30 Jun 2020 02:21:24: #1 total tags in treatment: 20128621 INFO @ Tue, 30 Jun 2020 02:21:24: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:21:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:21:25: #1 tags after filtering in treatment: 20128587 INFO @ Tue, 30 Jun 2020 02:21:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:21:25: #1 finished! INFO @ Tue, 30 Jun 2020 02:21:25: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:21:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:21:26: #2 number of paired peaks: 1131 INFO @ Tue, 30 Jun 2020 02:21:26: start model_add_line... INFO @ Tue, 30 Jun 2020 02:21:27: start X-correlation... INFO @ Tue, 30 Jun 2020 02:21:27: end of X-cor INFO @ Tue, 30 Jun 2020 02:21:27: #2 finished! INFO @ Tue, 30 Jun 2020 02:21:27: #2 predicted fragment length is 74 bps INFO @ Tue, 30 Jun 2020 02:21:27: #2 alternative fragment length(s) may be 3,74 bps INFO @ Tue, 30 Jun 2020 02:21:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2870713/SRX2870713.20_model.r WARNING @ Tue, 30 Jun 2020 02:21:27: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:21:27: #2 You may need to consider one of the other alternative d(s): 3,74 WARNING @ Tue, 30 Jun 2020 02:21:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:21:27: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:21:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:21:41: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:22:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2870713/SRX2870713.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:22:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2870713/SRX2870713.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:22:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2870713/SRX2870713.10_summits.bed INFO @ Tue, 30 Jun 2020 02:22:02: Done! pass1 - making usageList (701 chroms): 1 millis pass2 - checking and writing primary data (2450 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:22:08: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:22:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2870713/SRX2870713.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:22:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2870713/SRX2870713.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:22:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2870713/SRX2870713.20_summits.bed INFO @ Tue, 30 Jun 2020 02:22:29: Done! pass1 - making usageList (615 chroms): 2 millis pass2 - checking and writing primary data (1811 records, 4 fields): 19 millis CompletedMACS2peakCalling