Job ID = 6498609 SRX = SRX645118 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T00:02:40 prefetch.2.10.7: 1) Downloading 'SRR1505718'... 2020-06-26T00:02:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:12:34 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:12:34 prefetch.2.10.7: 1) 'SRR1505718' was downloaded successfully Read 42356426 spots for SRR1505718/SRR1505718.sra Written 42356426 spots for SRR1505718/SRR1505718.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: 00:18:56 42356426 reads; of these: 42356426 (100.00%) were unpaired; of these: 20076104 (47.40%) aligned 0 times 17848068 (42.14%) aligned exactly 1 time 4432254 (10.46%) aligned >1 times 52.60% overall alignment rate Time searching: 00:18:56 Overall time: 00:18:56 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 10983714 / 22280322 = 0.4930 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 @ Fri, 26 Jun 2020 09:42:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX645118/SRX645118.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX645118/SRX645118.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX645118/SRX645118.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX645118/SRX645118.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 @ Fri, 26 Jun 2020 09:42:40: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:42:40: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:42:47: 1000000 INFO @ Fri, 26 Jun 2020 09:42:54: 2000000 INFO @ Fri, 26 Jun 2020 09:43:01: 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 @ Fri, 26 Jun 2020 09:43:08: 4000000 INFO @ Fri, 26 Jun 2020 09:43:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX645118/SRX645118.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX645118/SRX645118.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX645118/SRX645118.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX645118/SRX645118.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 @ Fri, 26 Jun 2020 09:43:10: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:43:10: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:43:15: 5000000 INFO @ Fri, 26 Jun 2020 09:43:17: 1000000 INFO @ Fri, 26 Jun 2020 09:43:23: 6000000 INFO @ Fri, 26 Jun 2020 09:43:25: 2000000 INFO @ Fri, 26 Jun 2020 09:43:30: 7000000 INFO @ Fri, 26 Jun 2020 09:43:32: 3000000 INFO @ Fri, 26 Jun 2020 09:43:37: 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 @ Fri, 26 Jun 2020 09:43:40: 4000000 INFO @ Fri, 26 Jun 2020 09:43:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX645118/SRX645118.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX645118/SRX645118.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX645118/SRX645118.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX645118/SRX645118.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 @ Fri, 26 Jun 2020 09:43:40: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:43:40: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:43:45: 9000000 INFO @ Fri, 26 Jun 2020 09:43:47: 5000000 INFO @ Fri, 26 Jun 2020 09:43:48: 1000000 INFO @ Fri, 26 Jun 2020 09:43:52: 10000000 INFO @ Fri, 26 Jun 2020 09:43:55: 6000000 INFO @ Fri, 26 Jun 2020 09:43:55: 2000000 INFO @ Fri, 26 Jun 2020 09:44:00: 11000000 INFO @ Fri, 26 Jun 2020 09:44:02: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 09:44:02: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 09:44:02: #1 total tags in treatment: 11296608 INFO @ Fri, 26 Jun 2020 09:44:02: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:44:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:44:03: 7000000 INFO @ Fri, 26 Jun 2020 09:44:03: #1 tags after filtering in treatment: 11296608 INFO @ Fri, 26 Jun 2020 09:44:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:44:03: #1 finished! INFO @ Fri, 26 Jun 2020 09:44:03: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:44:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:44:03: 3000000 INFO @ Fri, 26 Jun 2020 09:44:04: #2 number of paired peaks: 1812 INFO @ Fri, 26 Jun 2020 09:44:04: start model_add_line... INFO @ Fri, 26 Jun 2020 09:44:04: start X-correlation... INFO @ Fri, 26 Jun 2020 09:44:04: end of X-cor INFO @ Fri, 26 Jun 2020 09:44:04: #2 finished! INFO @ Fri, 26 Jun 2020 09:44:04: #2 predicted fragment length is 118 bps INFO @ Fri, 26 Jun 2020 09:44:04: #2 alternative fragment length(s) may be 118 bps INFO @ Fri, 26 Jun 2020 09:44:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX645118/SRX645118.05_model.r WARNING @ Fri, 26 Jun 2020 09:44:04: #2 Since the d (118) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:44:04: #2 You may need to consider one of the other alternative d(s): 118 WARNING @ Fri, 26 Jun 2020 09:44:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 09:44:04: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:44:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:44:10: 8000000 INFO @ Fri, 26 Jun 2020 09:44:10: 4000000 INFO @ Fri, 26 Jun 2020 09:44:17: 9000000 INFO @ Fri, 26 Jun 2020 09:44:18: 5000000 INFO @ Fri, 26 Jun 2020 09:44:24: 10000000 INFO @ Fri, 26 Jun 2020 09:44:25: 6000000 INFO @ Fri, 26 Jun 2020 09:44:31: 11000000 INFO @ Fri, 26 Jun 2020 09:44:33: 7000000 INFO @ Fri, 26 Jun 2020 09:44:33: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:44:34: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 09:44:34: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 09:44:34: #1 total tags in treatment: 11296608 INFO @ Fri, 26 Jun 2020 09:44:34: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:44:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:44:34: #1 tags after filtering in treatment: 11296608 INFO @ Fri, 26 Jun 2020 09:44:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:44:34: #1 finished! INFO @ Fri, 26 Jun 2020 09:44:34: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:44:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:44:35: #2 number of paired peaks: 1812 INFO @ Fri, 26 Jun 2020 09:44:35: start model_add_line... INFO @ Fri, 26 Jun 2020 09:44:35: start X-correlation... INFO @ Fri, 26 Jun 2020 09:44:35: end of X-cor INFO @ Fri, 26 Jun 2020 09:44:35: #2 finished! INFO @ Fri, 26 Jun 2020 09:44:35: #2 predicted fragment length is 118 bps INFO @ Fri, 26 Jun 2020 09:44:35: #2 alternative fragment length(s) may be 118 bps INFO @ Fri, 26 Jun 2020 09:44:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX645118/SRX645118.10_model.r WARNING @ Fri, 26 Jun 2020 09:44:35: #2 Since the d (118) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:44:35: #2 You may need to consider one of the other alternative d(s): 118 WARNING @ Fri, 26 Jun 2020 09:44:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 09:44:35: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:44:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:44:40: 8000000 INFO @ Fri, 26 Jun 2020 09:44:47: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:44:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX645118/SRX645118.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:44:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX645118/SRX645118.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:44:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX645118/SRX645118.05_summits.bed INFO @ Fri, 26 Jun 2020 09:44:50: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9674 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:44:54: 10000000 INFO @ Fri, 26 Jun 2020 09:45:01: 11000000 INFO @ Fri, 26 Jun 2020 09:45:04: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 09:45:04: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 09:45:04: #1 total tags in treatment: 11296608 INFO @ Fri, 26 Jun 2020 09:45:04: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:45:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:45:04: #1 tags after filtering in treatment: 11296608 INFO @ Fri, 26 Jun 2020 09:45:04: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:45:04: #1 finished! INFO @ Fri, 26 Jun 2020 09:45:04: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:45:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:45:04: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:45:05: #2 number of paired peaks: 1812 INFO @ Fri, 26 Jun 2020 09:45:05: start model_add_line... INFO @ Fri, 26 Jun 2020 09:45:05: start X-correlation... INFO @ Fri, 26 Jun 2020 09:45:05: end of X-cor INFO @ Fri, 26 Jun 2020 09:45:05: #2 finished! INFO @ Fri, 26 Jun 2020 09:45:05: #2 predicted fragment length is 118 bps INFO @ Fri, 26 Jun 2020 09:45:05: #2 alternative fragment length(s) may be 118 bps INFO @ Fri, 26 Jun 2020 09:45:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX645118/SRX645118.20_model.r WARNING @ Fri, 26 Jun 2020 09:45:05: #2 Since the d (118) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:45:05: #2 You may need to consider one of the other alternative d(s): 118 WARNING @ Fri, 26 Jun 2020 09:45:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 09:45:05: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:45:05: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 09:45:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX645118/SRX645118.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:45:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX645118/SRX645118.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:45:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX645118/SRX645118.10_summits.bed INFO @ Fri, 26 Jun 2020 09:45:20: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6569 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:45:33: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:45:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX645118/SRX645118.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:45:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX645118/SRX645118.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:45:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX645118/SRX645118.20_summits.bed INFO @ Fri, 26 Jun 2020 09:45:49: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3425 records, 4 fields): 6 millis CompletedMACS2peakCalling