Job ID = 6457518 SRX = SRX4664669 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:53:36 prefetch.2.10.7: 1) Downloading 'SRR7813096'... 2020-06-21T11:53:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:56:47 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:56:47 prefetch.2.10.7: 1) 'SRR7813096' was downloaded successfully Read 25972202 spots for SRR7813096/SRR7813096.sra Written 25972202 spots for SRR7813096/SRR7813096.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: 00:07:52 25972202 reads; of these: 25972202 (100.00%) were unpaired; of these: 1057352 (4.07%) aligned 0 times 17489587 (67.34%) aligned exactly 1 time 7425263 (28.59%) aligned >1 times 95.93% overall alignment rate Time searching: 00:07:52 Overall time: 00:07:52 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 12 files... [bam_rmdupse_core] 4520253 / 24914850 = 0.1814 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 21:10:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4664669/SRX4664669.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4664669/SRX4664669.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4664669/SRX4664669.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4664669/SRX4664669.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 21:10:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:10:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:10:53: 1000000 INFO @ Sun, 21 Jun 2020 21:10:59: 2000000 INFO @ Sun, 21 Jun 2020 21:11:06: 3000000 INFO @ Sun, 21 Jun 2020 21:11:13: 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 21:11:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4664669/SRX4664669.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4664669/SRX4664669.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4664669/SRX4664669.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4664669/SRX4664669.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 21:11:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:11:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:11:21: 5000000 INFO @ Sun, 21 Jun 2020 21:11:23: 1000000 INFO @ Sun, 21 Jun 2020 21:11:28: 6000000 INFO @ Sun, 21 Jun 2020 21:11:30: 2000000 INFO @ Sun, 21 Jun 2020 21:11:36: 7000000 INFO @ Sun, 21 Jun 2020 21:11:38: 3000000 INFO @ Sun, 21 Jun 2020 21:11:44: 8000000 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 21:11:45: 4000000 INFO @ Sun, 21 Jun 2020 21:11:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4664669/SRX4664669.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4664669/SRX4664669.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4664669/SRX4664669.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4664669/SRX4664669.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 21:11:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:11:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:11:51: 9000000 INFO @ Sun, 21 Jun 2020 21:11:52: 5000000 INFO @ Sun, 21 Jun 2020 21:11:53: 1000000 INFO @ Sun, 21 Jun 2020 21:11:58: 10000000 INFO @ Sun, 21 Jun 2020 21:12:00: 6000000 INFO @ Sun, 21 Jun 2020 21:12:01: 2000000 INFO @ Sun, 21 Jun 2020 21:12:06: 11000000 INFO @ Sun, 21 Jun 2020 21:12:07: 7000000 INFO @ Sun, 21 Jun 2020 21:12:09: 3000000 INFO @ Sun, 21 Jun 2020 21:12:13: 12000000 INFO @ Sun, 21 Jun 2020 21:12:15: 8000000 INFO @ Sun, 21 Jun 2020 21:12:17: 4000000 INFO @ Sun, 21 Jun 2020 21:12:21: 13000000 INFO @ Sun, 21 Jun 2020 21:12:22: 9000000 INFO @ Sun, 21 Jun 2020 21:12:25: 5000000 INFO @ Sun, 21 Jun 2020 21:12:28: 14000000 INFO @ Sun, 21 Jun 2020 21:12:29: 10000000 INFO @ Sun, 21 Jun 2020 21:12:32: 6000000 INFO @ Sun, 21 Jun 2020 21:12:36: 15000000 INFO @ Sun, 21 Jun 2020 21:12:37: 11000000 INFO @ Sun, 21 Jun 2020 21:12:40: 7000000 INFO @ Sun, 21 Jun 2020 21:12:43: 16000000 INFO @ Sun, 21 Jun 2020 21:12:44: 12000000 INFO @ Sun, 21 Jun 2020 21:12:48: 8000000 INFO @ Sun, 21 Jun 2020 21:12:51: 17000000 INFO @ Sun, 21 Jun 2020 21:12:52: 13000000 INFO @ Sun, 21 Jun 2020 21:12:55: 9000000 INFO @ Sun, 21 Jun 2020 21:12:59: 14000000 INFO @ Sun, 21 Jun 2020 21:12:59: 18000000 INFO @ Sun, 21 Jun 2020 21:13:03: 10000000 INFO @ Sun, 21 Jun 2020 21:13:06: 15000000 INFO @ Sun, 21 Jun 2020 21:13:07: 19000000 INFO @ Sun, 21 Jun 2020 21:13:11: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:13:14: 16000000 INFO @ Sun, 21 Jun 2020 21:13:14: 20000000 INFO @ Sun, 21 Jun 2020 21:13:17: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:13:17: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:13:17: #1 total tags in treatment: 20394597 INFO @ Sun, 21 Jun 2020 21:13:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:13:17: #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 21:13:18: #1 tags after filtering in treatment: 20394537 INFO @ Sun, 21 Jun 2020 21:13:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:13:18: #1 finished! INFO @ Sun, 21 Jun 2020 21:13:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:13:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:13:18: 12000000 INFO @ Sun, 21 Jun 2020 21:13:19: #2 number of paired peaks: 1284 INFO @ Sun, 21 Jun 2020 21:13:19: start model_add_line... INFO @ Sun, 21 Jun 2020 21:13:20: start X-correlation... INFO @ Sun, 21 Jun 2020 21:13:20: end of X-cor INFO @ Sun, 21 Jun 2020 21:13:20: #2 finished! INFO @ Sun, 21 Jun 2020 21:13:20: #2 predicted fragment length is 76 bps INFO @ Sun, 21 Jun 2020 21:13:20: #2 alternative fragment length(s) may be 2,76,558 bps INFO @ Sun, 21 Jun 2020 21:13:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4664669/SRX4664669.05_model.r WARNING @ Sun, 21 Jun 2020 21:13:20: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:13:20: #2 You may need to consider one of the other alternative d(s): 2,76,558 WARNING @ Sun, 21 Jun 2020 21:13:20: #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 21:13:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:13:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:13:21: 17000000 INFO @ Sun, 21 Jun 2020 21:13:26: 13000000 INFO @ Sun, 21 Jun 2020 21:13:29: 18000000 INFO @ Sun, 21 Jun 2020 21:13:34: 14000000 INFO @ Sun, 21 Jun 2020 21:13:36: 19000000 INFO @ Sun, 21 Jun 2020 21:13:41: 15000000 INFO @ Sun, 21 Jun 2020 21:13:44: 20000000 INFO @ Sun, 21 Jun 2020 21:13:47: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:13:47: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:13:47: #1 total tags in treatment: 20394597 INFO @ Sun, 21 Jun 2020 21:13:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:13:47: #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 21:13:48: #1 tags after filtering in treatment: 20394537 INFO @ Sun, 21 Jun 2020 21:13:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:13:48: #1 finished! INFO @ Sun, 21 Jun 2020 21:13:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:13:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:13:49: 16000000 INFO @ Sun, 21 Jun 2020 21:13:49: #2 number of paired peaks: 1284 INFO @ Sun, 21 Jun 2020 21:13:49: start model_add_line... INFO @ Sun, 21 Jun 2020 21:13:49: start X-correlation... INFO @ Sun, 21 Jun 2020 21:13:49: end of X-cor INFO @ Sun, 21 Jun 2020 21:13:49: #2 finished! INFO @ Sun, 21 Jun 2020 21:13:49: #2 predicted fragment length is 76 bps INFO @ Sun, 21 Jun 2020 21:13:49: #2 alternative fragment length(s) may be 2,76,558 bps INFO @ Sun, 21 Jun 2020 21:13:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4664669/SRX4664669.10_model.r WARNING @ Sun, 21 Jun 2020 21:13:49: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:13:49: #2 You may need to consider one of the other alternative d(s): 2,76,558 WARNING @ Sun, 21 Jun 2020 21:13:49: #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 21:13:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:13:49: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:13:56: 17000000 INFO @ Sun, 21 Jun 2020 21:13:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:14:03: 18000000 INFO @ Sun, 21 Jun 2020 21:14:10: 19000000 INFO @ Sun, 21 Jun 2020 21:14:17: 20000000 INFO @ Sun, 21 Jun 2020 21:14:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4664669/SRX4664669.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:14:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4664669/SRX4664669.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:14:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4664669/SRX4664669.05_summits.bed INFO @ Sun, 21 Jun 2020 21:14:18: Done! pass1 - making usageList (589 chroms): 2 millis pass2 - checking and writing primary data (4708 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:14:20: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:14:20: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:14:20: #1 total tags in treatment: 20394597 INFO @ Sun, 21 Jun 2020 21:14:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:14:20: #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 21:14:21: #1 tags after filtering in treatment: 20394537 INFO @ Sun, 21 Jun 2020 21:14:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:14:21: #1 finished! INFO @ Sun, 21 Jun 2020 21:14:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:14:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:14:22: #2 number of paired peaks: 1284 INFO @ Sun, 21 Jun 2020 21:14:22: start model_add_line... INFO @ Sun, 21 Jun 2020 21:14:22: start X-correlation... INFO @ Sun, 21 Jun 2020 21:14:22: end of X-cor INFO @ Sun, 21 Jun 2020 21:14:22: #2 finished! INFO @ Sun, 21 Jun 2020 21:14:22: #2 predicted fragment length is 76 bps INFO @ Sun, 21 Jun 2020 21:14:22: #2 alternative fragment length(s) may be 2,76,558 bps INFO @ Sun, 21 Jun 2020 21:14:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4664669/SRX4664669.20_model.r WARNING @ Sun, 21 Jun 2020 21:14:22: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:14:22: #2 You may need to consider one of the other alternative d(s): 2,76,558 WARNING @ Sun, 21 Jun 2020 21:14:22: #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 21:14:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:14:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:14:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:14:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4664669/SRX4664669.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:14:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4664669/SRX4664669.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:14:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4664669/SRX4664669.10_summits.bed INFO @ Sun, 21 Jun 2020 21:14:49: Done! pass1 - making usageList (517 chroms): 1 millis pass2 - checking and writing primary data (2892 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:15:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:15:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4664669/SRX4664669.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:15:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4664669/SRX4664669.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:15:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4664669/SRX4664669.20_summits.bed INFO @ Sun, 21 Jun 2020 21:15:21: Done! pass1 - making usageList (384 chroms): 1 millis pass2 - checking and writing primary data (1544 records, 4 fields): 13 millis CompletedMACS2peakCalling