Job ID = 6457835 SRX = SRX4801800 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:17:22 prefetch.2.10.7: 1) Downloading 'SRR7968385'... 2020-06-21T12:17:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:20:13 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:20:13 prefetch.2.10.7: 1) 'SRR7968385' was downloaded successfully Read 19545165 spots for SRR7968385/SRR7968385.sra Written 19545165 spots for SRR7968385/SRR7968385.sra 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: 00:06:37 19545165 reads; of these: 19545165 (100.00%) were unpaired; of these: 516788 (2.64%) aligned 0 times 13119998 (67.13%) aligned exactly 1 time 5908379 (30.23%) aligned >1 times 97.36% overall alignment rate Time searching: 00:06:37 Overall time: 00:06:37 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 8 files... [bam_rmdupse_core] 2540483 / 19028377 = 0.1335 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 @ Sun, 21 Jun 2020 21:33:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4801800/SRX4801800.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4801800/SRX4801800.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4801800/SRX4801800.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4801800/SRX4801800.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 @ Sun, 21 Jun 2020 21:33:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:33:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:33:15: 1000000 INFO @ Sun, 21 Jun 2020 21:33:21: 2000000 INFO @ Sun, 21 Jun 2020 21:33:27: 3000000 INFO @ Sun, 21 Jun 2020 21:33:33: 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 @ Sun, 21 Jun 2020 21:33:39: 5000000 INFO @ Sun, 21 Jun 2020 21:33:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4801800/SRX4801800.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4801800/SRX4801800.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4801800/SRX4801800.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4801800/SRX4801800.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 @ Sun, 21 Jun 2020 21:33:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:33:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:33:45: 6000000 INFO @ Sun, 21 Jun 2020 21:33:48: 1000000 INFO @ Sun, 21 Jun 2020 21:33:52: 7000000 INFO @ Sun, 21 Jun 2020 21:33:55: 2000000 INFO @ Sun, 21 Jun 2020 21:33:59: 8000000 INFO @ Sun, 21 Jun 2020 21:34:03: 3000000 INFO @ Sun, 21 Jun 2020 21:34:06: 9000000 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 @ Sun, 21 Jun 2020 21:34:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4801800/SRX4801800.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4801800/SRX4801800.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4801800/SRX4801800.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4801800/SRX4801800.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 @ Sun, 21 Jun 2020 21:34:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:34:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:34:10: 4000000 INFO @ Sun, 21 Jun 2020 21:34:13: 10000000 INFO @ Sun, 21 Jun 2020 21:34:18: 1000000 INFO @ Sun, 21 Jun 2020 21:34:18: 5000000 INFO @ Sun, 21 Jun 2020 21:34:20: 11000000 INFO @ Sun, 21 Jun 2020 21:34:26: 2000000 INFO @ Sun, 21 Jun 2020 21:34:26: 6000000 INFO @ Sun, 21 Jun 2020 21:34:27: 12000000 INFO @ Sun, 21 Jun 2020 21:34:34: 3000000 INFO @ Sun, 21 Jun 2020 21:34:34: 13000000 INFO @ Sun, 21 Jun 2020 21:34:34: 7000000 INFO @ Sun, 21 Jun 2020 21:34:41: 14000000 INFO @ Sun, 21 Jun 2020 21:34:41: 4000000 INFO @ Sun, 21 Jun 2020 21:34:42: 8000000 INFO @ Sun, 21 Jun 2020 21:34:48: 15000000 INFO @ Sun, 21 Jun 2020 21:34:49: 5000000 INFO @ Sun, 21 Jun 2020 21:34:50: 9000000 INFO @ Sun, 21 Jun 2020 21:34:55: 16000000 INFO @ Sun, 21 Jun 2020 21:34:57: 6000000 INFO @ Sun, 21 Jun 2020 21:34:58: 10000000 INFO @ Sun, 21 Jun 2020 21:34:59: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 21:34:59: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 21:34:59: #1 total tags in treatment: 16487894 INFO @ Sun, 21 Jun 2020 21:34:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:34:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 21:34:59: #1 tags after filtering in treatment: 16487796 INFO @ Sun, 21 Jun 2020 21:34:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:34:59: #1 finished! INFO @ Sun, 21 Jun 2020 21:34:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:34:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:35:01: #2 number of paired peaks: 1411 INFO @ Sun, 21 Jun 2020 21:35:01: start model_add_line... INFO @ Sun, 21 Jun 2020 21:35:01: start X-correlation... INFO @ Sun, 21 Jun 2020 21:35:01: end of X-cor INFO @ Sun, 21 Jun 2020 21:35:01: #2 finished! INFO @ Sun, 21 Jun 2020 21:35:01: #2 predicted fragment length is 71 bps INFO @ Sun, 21 Jun 2020 21:35:01: #2 alternative fragment length(s) may be 2,71 bps INFO @ Sun, 21 Jun 2020 21:35:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4801800/SRX4801800.05_model.r WARNING @ Sun, 21 Jun 2020 21:35:01: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:35:01: #2 You may need to consider one of the other alternative d(s): 2,71 WARNING @ Sun, 21 Jun 2020 21:35:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 21:35:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:35:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:35:05: 7000000 INFO @ Sun, 21 Jun 2020 21:35:06: 11000000 INFO @ Sun, 21 Jun 2020 21:35:13: 8000000 INFO @ Sun, 21 Jun 2020 21:35:14: 12000000 INFO @ Sun, 21 Jun 2020 21:35:21: 9000000 INFO @ Sun, 21 Jun 2020 21:35:22: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:35:29: 10000000 INFO @ Sun, 21 Jun 2020 21:35:30: 14000000 INFO @ Sun, 21 Jun 2020 21:35:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:35:37: 11000000 INFO @ Sun, 21 Jun 2020 21:35:39: 15000000 INFO @ Sun, 21 Jun 2020 21:35:45: 12000000 INFO @ Sun, 21 Jun 2020 21:35:46: 16000000 INFO @ Sun, 21 Jun 2020 21:35:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4801800/SRX4801800.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:35:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4801800/SRX4801800.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:35:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4801800/SRX4801800.05_summits.bed INFO @ Sun, 21 Jun 2020 21:35:49: Done! pass1 - making usageList (608 chroms): 1 millis pass2 - checking and writing primary data (3114 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:35:50: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 21:35:50: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 21:35:50: #1 total tags in treatment: 16487894 INFO @ Sun, 21 Jun 2020 21:35:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:35:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 21:35:51: #1 tags after filtering in treatment: 16487796 INFO @ Sun, 21 Jun 2020 21:35:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:35:51: #1 finished! INFO @ Sun, 21 Jun 2020 21:35:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:35:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:35:52: #2 number of paired peaks: 1411 INFO @ Sun, 21 Jun 2020 21:35:52: start model_add_line... INFO @ Sun, 21 Jun 2020 21:35:52: start X-correlation... INFO @ Sun, 21 Jun 2020 21:35:52: end of X-cor INFO @ Sun, 21 Jun 2020 21:35:52: #2 finished! INFO @ Sun, 21 Jun 2020 21:35:52: #2 predicted fragment length is 71 bps INFO @ Sun, 21 Jun 2020 21:35:52: #2 alternative fragment length(s) may be 2,71 bps INFO @ Sun, 21 Jun 2020 21:35:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4801800/SRX4801800.10_model.r WARNING @ Sun, 21 Jun 2020 21:35:52: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:35:52: #2 You may need to consider one of the other alternative d(s): 2,71 WARNING @ Sun, 21 Jun 2020 21:35:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 21:35:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:35:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:35:53: 13000000 INFO @ Sun, 21 Jun 2020 21:36:01: 14000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:36:08: 15000000 INFO @ Sun, 21 Jun 2020 21:36:15: 16000000 INFO @ Sun, 21 Jun 2020 21:36:19: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 21:36:19: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 21:36:19: #1 total tags in treatment: 16487894 INFO @ Sun, 21 Jun 2020 21:36:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:36:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 21:36:19: #1 tags after filtering in treatment: 16487796 INFO @ Sun, 21 Jun 2020 21:36:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:36:19: #1 finished! INFO @ Sun, 21 Jun 2020 21:36:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:36:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:36:20: #2 number of paired peaks: 1411 INFO @ Sun, 21 Jun 2020 21:36:20: start model_add_line... INFO @ Sun, 21 Jun 2020 21:36:21: start X-correlation... INFO @ Sun, 21 Jun 2020 21:36:21: end of X-cor INFO @ Sun, 21 Jun 2020 21:36:21: #2 finished! INFO @ Sun, 21 Jun 2020 21:36:21: #2 predicted fragment length is 71 bps INFO @ Sun, 21 Jun 2020 21:36:21: #2 alternative fragment length(s) may be 2,71 bps INFO @ Sun, 21 Jun 2020 21:36:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4801800/SRX4801800.20_model.r WARNING @ Sun, 21 Jun 2020 21:36:21: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:36:21: #2 You may need to consider one of the other alternative d(s): 2,71 WARNING @ Sun, 21 Jun 2020 21:36:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 21:36:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:36:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:36:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:36:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4801800/SRX4801800.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:36:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4801800/SRX4801800.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:36:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4801800/SRX4801800.10_summits.bed INFO @ Sun, 21 Jun 2020 21:36:40: Done! pass1 - making usageList (506 chroms): 1 millis pass2 - checking and writing primary data (1862 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:36:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:37:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4801800/SRX4801800.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:37:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4801800/SRX4801800.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:37:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4801800/SRX4801800.20_summits.bed INFO @ Sun, 21 Jun 2020 21:37:10: Done! pass1 - making usageList (328 chroms): 1 millis pass2 - checking and writing primary data (770 records, 4 fields): 11 millis CompletedMACS2peakCalling