Job ID = 6454629 SRX = SRX2422633 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:21:59 prefetch.2.10.7: 1) Downloading 'SRR5110247'... 2020-06-21T09:21:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:24:22 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:24:22 prefetch.2.10.7: 'SRR5110247' is valid 2020-06-21T09:24:22 prefetch.2.10.7: 1) 'SRR5110247' was downloaded successfully Read 13520069 spots for SRR5110247/SRR5110247.sra Written 13520069 spots for SRR5110247/SRR5110247.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: 00:04:29 13520069 reads; of these: 13520069 (100.00%) were unpaired; of these: 540592 (4.00%) aligned 0 times 9015503 (66.68%) aligned exactly 1 time 3963974 (29.32%) aligned >1 times 96.00% overall alignment rate Time searching: 00:04:29 Overall time: 00:04:29 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] 1674065 / 12979477 = 0.1290 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 18:33:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2422633/SRX2422633.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2422633/SRX2422633.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2422633/SRX2422633.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2422633/SRX2422633.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 18:33:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:33:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:33:28: 1000000 INFO @ Sun, 21 Jun 2020 18:33:34: 2000000 INFO @ Sun, 21 Jun 2020 18:33:41: 3000000 INFO @ Sun, 21 Jun 2020 18:33:47: 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 @ Sun, 21 Jun 2020 18:33:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2422633/SRX2422633.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2422633/SRX2422633.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2422633/SRX2422633.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2422633/SRX2422633.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 18:33:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:33:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:33:53: 5000000 INFO @ Sun, 21 Jun 2020 18:33:59: 1000000 INFO @ Sun, 21 Jun 2020 18:34:00: 6000000 INFO @ Sun, 21 Jun 2020 18:34:06: 2000000 INFO @ Sun, 21 Jun 2020 18:34:07: 7000000 INFO @ Sun, 21 Jun 2020 18:34:13: 3000000 INFO @ Sun, 21 Jun 2020 18:34:14: 8000000 INFO @ Sun, 21 Jun 2020 18:34:20: 4000000 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 18:34:21: 9000000 INFO @ Sun, 21 Jun 2020 18:34:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2422633/SRX2422633.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2422633/SRX2422633.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2422633/SRX2422633.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2422633/SRX2422633.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 18:34:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:34:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:34:27: 5000000 INFO @ Sun, 21 Jun 2020 18:34:28: 10000000 INFO @ Sun, 21 Jun 2020 18:34:30: 1000000 INFO @ Sun, 21 Jun 2020 18:34:35: 6000000 INFO @ Sun, 21 Jun 2020 18:34:36: 11000000 INFO @ Sun, 21 Jun 2020 18:34:37: 2000000 INFO @ Sun, 21 Jun 2020 18:34:38: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 18:34:38: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 18:34:38: #1 total tags in treatment: 11305412 INFO @ Sun, 21 Jun 2020 18:34:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:34:38: #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 18:34:39: #1 tags after filtering in treatment: 11305293 INFO @ Sun, 21 Jun 2020 18:34:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:34:39: #1 finished! INFO @ Sun, 21 Jun 2020 18:34:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:34:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:34:39: #2 number of paired peaks: 1572 INFO @ Sun, 21 Jun 2020 18:34:39: start model_add_line... INFO @ Sun, 21 Jun 2020 18:34:40: start X-correlation... INFO @ Sun, 21 Jun 2020 18:34:40: end of X-cor INFO @ Sun, 21 Jun 2020 18:34:40: #2 finished! INFO @ Sun, 21 Jun 2020 18:34:40: #2 predicted fragment length is 78 bps INFO @ Sun, 21 Jun 2020 18:34:40: #2 alternative fragment length(s) may be 4,78,583,596 bps INFO @ Sun, 21 Jun 2020 18:34:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2422633/SRX2422633.05_model.r WARNING @ Sun, 21 Jun 2020 18:34:40: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:34:40: #2 You may need to consider one of the other alternative d(s): 4,78,583,596 WARNING @ Sun, 21 Jun 2020 18:34:40: #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 18:34:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:34:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:34:42: 7000000 INFO @ Sun, 21 Jun 2020 18:34:45: 3000000 INFO @ Sun, 21 Jun 2020 18:34:49: 8000000 INFO @ Sun, 21 Jun 2020 18:34:52: 4000000 INFO @ Sun, 21 Jun 2020 18:34:57: 9000000 INFO @ Sun, 21 Jun 2020 18:34:59: 5000000 INFO @ Sun, 21 Jun 2020 18:35:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:35:04: 10000000 INFO @ Sun, 21 Jun 2020 18:35:06: 6000000 INFO @ Sun, 21 Jun 2020 18:35:11: 11000000 INFO @ Sun, 21 Jun 2020 18:35:13: 7000000 INFO @ Sun, 21 Jun 2020 18:35:13: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 18:35:13: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 18:35:13: #1 total tags in treatment: 11305412 INFO @ Sun, 21 Jun 2020 18:35:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:35:13: #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 18:35:14: #1 tags after filtering in treatment: 11305293 INFO @ Sun, 21 Jun 2020 18:35:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:35:14: #1 finished! INFO @ Sun, 21 Jun 2020 18:35:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:35:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:35:15: #2 number of paired peaks: 1572 INFO @ Sun, 21 Jun 2020 18:35:15: start model_add_line... INFO @ Sun, 21 Jun 2020 18:35:15: start X-correlation... INFO @ Sun, 21 Jun 2020 18:35:15: end of X-cor INFO @ Sun, 21 Jun 2020 18:35:15: #2 finished! INFO @ Sun, 21 Jun 2020 18:35:15: #2 predicted fragment length is 78 bps INFO @ Sun, 21 Jun 2020 18:35:15: #2 alternative fragment length(s) may be 4,78,583,596 bps INFO @ Sun, 21 Jun 2020 18:35:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2422633/SRX2422633.10_model.r WARNING @ Sun, 21 Jun 2020 18:35:15: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:35:15: #2 You may need to consider one of the other alternative d(s): 4,78,583,596 WARNING @ Sun, 21 Jun 2020 18:35:15: #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 18:35:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:35:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:35:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2422633/SRX2422633.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:35:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2422633/SRX2422633.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:35:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2422633/SRX2422633.05_summits.bed INFO @ Sun, 21 Jun 2020 18:35:16: Done! pass1 - making usageList (606 chroms): 2 millis pass2 - checking and writing primary data (2935 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:35:19: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:35:26: 9000000 INFO @ Sun, 21 Jun 2020 18:35:32: 10000000 INFO @ Sun, 21 Jun 2020 18:35:39: 11000000 INFO @ Sun, 21 Jun 2020 18:35:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:35:41: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 18:35:41: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 18:35:41: #1 total tags in treatment: 11305412 INFO @ Sun, 21 Jun 2020 18:35:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:35:41: #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 18:35:41: #1 tags after filtering in treatment: 11305293 INFO @ Sun, 21 Jun 2020 18:35:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:35:41: #1 finished! INFO @ Sun, 21 Jun 2020 18:35:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:35:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:35:42: #2 number of paired peaks: 1572 INFO @ Sun, 21 Jun 2020 18:35:42: start model_add_line... INFO @ Sun, 21 Jun 2020 18:35:42: start X-correlation... INFO @ Sun, 21 Jun 2020 18:35:42: end of X-cor INFO @ Sun, 21 Jun 2020 18:35:42: #2 finished! INFO @ Sun, 21 Jun 2020 18:35:42: #2 predicted fragment length is 78 bps INFO @ Sun, 21 Jun 2020 18:35:42: #2 alternative fragment length(s) may be 4,78,583,596 bps INFO @ Sun, 21 Jun 2020 18:35:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2422633/SRX2422633.20_model.r WARNING @ Sun, 21 Jun 2020 18:35:42: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:35:42: #2 You may need to consider one of the other alternative d(s): 4,78,583,596 WARNING @ Sun, 21 Jun 2020 18:35:42: #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 18:35:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:35:42: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:35:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2422633/SRX2422633.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:35:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2422633/SRX2422633.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:35:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2422633/SRX2422633.10_summits.bed INFO @ Sun, 21 Jun 2020 18:35:51: Done! pass1 - making usageList (473 chroms): 1 millis pass2 - checking and writing primary data (1575 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:36:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:36:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2422633/SRX2422633.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:36:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2422633/SRX2422633.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:36:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2422633/SRX2422633.20_summits.bed INFO @ Sun, 21 Jun 2020 18:36:16: Done! pass1 - making usageList (280 chroms): 0 millis pass2 - checking and writing primary data (624 records, 4 fields): 10 millis CompletedMACS2peakCalling