Job ID = 6453807 SRX = SRX149193 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:41:17 prefetch.2.10.7: 1) Downloading 'SRR500153'... 2020-06-21T08:41:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:43:05 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:43:06 prefetch.2.10.7: 'SRR500153' is valid 2020-06-21T08:43:06 prefetch.2.10.7: 1) 'SRR500153' was downloaded successfully Read 16997463 spots for SRR500153/SRR500153.sra Written 16997463 spots for SRR500153/SRR500153.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: 00:04:15 16997463 reads; of these: 16997463 (100.00%) were unpaired; of these: 890378 (5.24%) aligned 0 times 10524941 (61.92%) aligned exactly 1 time 5582144 (32.84%) aligned >1 times 94.76% overall alignment rate Time searching: 00:04:15 Overall time: 00:04:15 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] 2756432 / 16107085 = 0.1711 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 17:52:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX149193/SRX149193.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX149193/SRX149193.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX149193/SRX149193.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX149193/SRX149193.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 17:52:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:52:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:52:07: 1000000 INFO @ Sun, 21 Jun 2020 17:52:12: 2000000 INFO @ Sun, 21 Jun 2020 17:52:17: 3000000 INFO @ Sun, 21 Jun 2020 17:52:22: 4000000 INFO @ Sun, 21 Jun 2020 17:52:27: 5000000 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 17:52:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX149193/SRX149193.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX149193/SRX149193.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX149193/SRX149193.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX149193/SRX149193.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 17:52:32: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:52:32: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:52:33: 6000000 INFO @ Sun, 21 Jun 2020 17:52:37: 1000000 INFO @ Sun, 21 Jun 2020 17:52:38: 7000000 INFO @ Sun, 21 Jun 2020 17:52:43: 2000000 INFO @ Sun, 21 Jun 2020 17:52:43: 8000000 INFO @ Sun, 21 Jun 2020 17:52:48: 3000000 INFO @ Sun, 21 Jun 2020 17:52:48: 9000000 INFO @ Sun, 21 Jun 2020 17:52:53: 4000000 INFO @ Sun, 21 Jun 2020 17:52:54: 10000000 INFO @ Sun, 21 Jun 2020 17:52:59: 5000000 INFO @ Sun, 21 Jun 2020 17:52:59: 11000000 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 17:53:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX149193/SRX149193.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX149193/SRX149193.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX149193/SRX149193.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX149193/SRX149193.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 17:53:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:53:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:53:04: 6000000 INFO @ Sun, 21 Jun 2020 17:53:04: 12000000 INFO @ Sun, 21 Jun 2020 17:53:07: 1000000 INFO @ Sun, 21 Jun 2020 17:53:09: 7000000 INFO @ Sun, 21 Jun 2020 17:53:10: 13000000 INFO @ Sun, 21 Jun 2020 17:53:12: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:53:12: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:53:12: #1 total tags in treatment: 13350653 INFO @ Sun, 21 Jun 2020 17:53:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:53:12: #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 17:53:12: #1 tags after filtering in treatment: 13350599 INFO @ Sun, 21 Jun 2020 17:53:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:53:12: #1 finished! INFO @ Sun, 21 Jun 2020 17:53:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:53:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:53:13: 2000000 INFO @ Sun, 21 Jun 2020 17:53:13: #2 number of paired peaks: 1567 INFO @ Sun, 21 Jun 2020 17:53:13: start model_add_line... INFO @ Sun, 21 Jun 2020 17:53:13: start X-correlation... INFO @ Sun, 21 Jun 2020 17:53:13: end of X-cor INFO @ Sun, 21 Jun 2020 17:53:13: #2 finished! INFO @ Sun, 21 Jun 2020 17:53:13: #2 predicted fragment length is 38 bps INFO @ Sun, 21 Jun 2020 17:53:13: #2 alternative fragment length(s) may be 2,38,559,575 bps INFO @ Sun, 21 Jun 2020 17:53:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX149193/SRX149193.05_model.r WARNING @ Sun, 21 Jun 2020 17:53:13: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:53:13: #2 You may need to consider one of the other alternative d(s): 2,38,559,575 WARNING @ Sun, 21 Jun 2020 17:53:13: #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 17:53:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:53:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:53:14: 8000000 INFO @ Sun, 21 Jun 2020 17:53:18: 3000000 INFO @ Sun, 21 Jun 2020 17:53:20: 9000000 INFO @ Sun, 21 Jun 2020 17:53:23: 4000000 INFO @ Sun, 21 Jun 2020 17:53:25: 10000000 INFO @ Sun, 21 Jun 2020 17:53:28: 5000000 INFO @ Sun, 21 Jun 2020 17:53:30: 11000000 INFO @ Sun, 21 Jun 2020 17:53:33: 6000000 INFO @ Sun, 21 Jun 2020 17:53:36: 12000000 INFO @ Sun, 21 Jun 2020 17:53:39: 7000000 INFO @ Sun, 21 Jun 2020 17:53:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:53:41: 13000000 INFO @ Sun, 21 Jun 2020 17:53:43: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:53:43: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:53:43: #1 total tags in treatment: 13350653 INFO @ Sun, 21 Jun 2020 17:53:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:53:43: #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 17:53:43: #1 tags after filtering in treatment: 13350599 INFO @ Sun, 21 Jun 2020 17:53:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:53:43: #1 finished! INFO @ Sun, 21 Jun 2020 17:53:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:53:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:53:44: 8000000 INFO @ Sun, 21 Jun 2020 17:53:44: #2 number of paired peaks: 1567 INFO @ Sun, 21 Jun 2020 17:53:44: start model_add_line... INFO @ Sun, 21 Jun 2020 17:53:45: start X-correlation... INFO @ Sun, 21 Jun 2020 17:53:45: end of X-cor INFO @ Sun, 21 Jun 2020 17:53:45: #2 finished! INFO @ Sun, 21 Jun 2020 17:53:45: #2 predicted fragment length is 38 bps INFO @ Sun, 21 Jun 2020 17:53:45: #2 alternative fragment length(s) may be 2,38,559,575 bps INFO @ Sun, 21 Jun 2020 17:53:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX149193/SRX149193.10_model.r WARNING @ Sun, 21 Jun 2020 17:53:45: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:53:45: #2 You may need to consider one of the other alternative d(s): 2,38,559,575 WARNING @ Sun, 21 Jun 2020 17:53:45: #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 17:53:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:53:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:53:49: 9000000 INFO @ Sun, 21 Jun 2020 17:53:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX149193/SRX149193.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:53:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX149193/SRX149193.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:53:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX149193/SRX149193.05_summits.bed INFO @ Sun, 21 Jun 2020 17:53:52: Done! pass1 - making usageList (615 chroms): 2 millis pass2 - checking and writing primary data (3051 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:53:54: 10000000 INFO @ Sun, 21 Jun 2020 17:53:59: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:54:04: 12000000 INFO @ Sun, 21 Jun 2020 17:54:09: 13000000 INFO @ Sun, 21 Jun 2020 17:54:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:54:10: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:54:10: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:54:10: #1 total tags in treatment: 13350653 INFO @ Sun, 21 Jun 2020 17:54:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:54:10: #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 17:54:11: #1 tags after filtering in treatment: 13350599 INFO @ Sun, 21 Jun 2020 17:54:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:54:11: #1 finished! INFO @ Sun, 21 Jun 2020 17:54:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:54:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:54:12: #2 number of paired peaks: 1567 INFO @ Sun, 21 Jun 2020 17:54:12: start model_add_line... INFO @ Sun, 21 Jun 2020 17:54:12: start X-correlation... INFO @ Sun, 21 Jun 2020 17:54:12: end of X-cor INFO @ Sun, 21 Jun 2020 17:54:12: #2 finished! INFO @ Sun, 21 Jun 2020 17:54:12: #2 predicted fragment length is 38 bps INFO @ Sun, 21 Jun 2020 17:54:12: #2 alternative fragment length(s) may be 2,38,559,575 bps INFO @ Sun, 21 Jun 2020 17:54:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX149193/SRX149193.20_model.r WARNING @ Sun, 21 Jun 2020 17:54:12: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:54:12: #2 You may need to consider one of the other alternative d(s): 2,38,559,575 WARNING @ Sun, 21 Jun 2020 17:54:12: #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 17:54:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:54:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:54:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX149193/SRX149193.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:54:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX149193/SRX149193.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:54:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX149193/SRX149193.10_summits.bed INFO @ Sun, 21 Jun 2020 17:54:23: Done! pass1 - making usageList (512 chroms): 1 millis pass2 - checking and writing primary data (2156 records, 4 fields): 15 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:54:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:54:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX149193/SRX149193.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:54:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX149193/SRX149193.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:54:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX149193/SRX149193.20_summits.bed INFO @ Sun, 21 Jun 2020 17:54:51: Done! pass1 - making usageList (235 chroms): 1 millis pass2 - checking and writing primary data (521 records, 4 fields): 8 millis CompletedMACS2peakCalling