Job ID = 6457483 SRX = SRX4664641 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:44:51 prefetch.2.10.7: 1) Downloading 'SRR7813068'... 2020-06-21T11:44:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:47:45 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:47:46 prefetch.2.10.7: 'SRR7813068' is valid 2020-06-21T11:47:46 prefetch.2.10.7: 1) 'SRR7813068' was downloaded successfully Read 21874226 spots for SRR7813068/SRR7813068.sra Written 21874226 spots for SRR7813068/SRR7813068.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: 00:06:51 21874226 reads; of these: 21874226 (100.00%) were unpaired; of these: 668191 (3.05%) aligned 0 times 14363263 (65.66%) aligned exactly 1 time 6842772 (31.28%) aligned >1 times 96.95% overall alignment rate Time searching: 00:06:51 Overall time: 00:06:51 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] 3810963 / 21206035 = 0.1797 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 21:00:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4664641/SRX4664641.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4664641/SRX4664641.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4664641/SRX4664641.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4664641/SRX4664641.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 21:00:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:00:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:00:09: 1000000 INFO @ Sun, 21 Jun 2020 21:00:15: 2000000 INFO @ Sun, 21 Jun 2020 21:00:21: 3000000 INFO @ Sun, 21 Jun 2020 21:00:27: 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 21:00:33: 5000000 INFO @ Sun, 21 Jun 2020 21:00:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4664641/SRX4664641.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4664641/SRX4664641.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4664641/SRX4664641.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4664641/SRX4664641.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 21:00:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:00:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:00:38: 1000000 INFO @ Sun, 21 Jun 2020 21:00:38: 6000000 INFO @ Sun, 21 Jun 2020 21:00:44: 2000000 INFO @ Sun, 21 Jun 2020 21:00:44: 7000000 INFO @ Sun, 21 Jun 2020 21:00:49: 3000000 INFO @ Sun, 21 Jun 2020 21:00:51: 8000000 INFO @ Sun, 21 Jun 2020 21:00:54: 4000000 INFO @ Sun, 21 Jun 2020 21:00:57: 9000000 INFO @ Sun, 21 Jun 2020 21:01:00: 5000000 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 21:01:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4664641/SRX4664641.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4664641/SRX4664641.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4664641/SRX4664641.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4664641/SRX4664641.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 21:01:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:01:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:01:03: 10000000 INFO @ Sun, 21 Jun 2020 21:01:05: 6000000 INFO @ Sun, 21 Jun 2020 21:01:08: 1000000 INFO @ Sun, 21 Jun 2020 21:01:09: 11000000 INFO @ Sun, 21 Jun 2020 21:01:10: 7000000 INFO @ Sun, 21 Jun 2020 21:01:14: 2000000 INFO @ Sun, 21 Jun 2020 21:01:15: 12000000 INFO @ Sun, 21 Jun 2020 21:01:16: 8000000 INFO @ Sun, 21 Jun 2020 21:01:19: 3000000 INFO @ Sun, 21 Jun 2020 21:01:21: 9000000 INFO @ Sun, 21 Jun 2020 21:01:22: 13000000 INFO @ Sun, 21 Jun 2020 21:01:25: 4000000 INFO @ Sun, 21 Jun 2020 21:01:27: 10000000 INFO @ Sun, 21 Jun 2020 21:01:28: 14000000 INFO @ Sun, 21 Jun 2020 21:01:30: 5000000 INFO @ Sun, 21 Jun 2020 21:01:32: 11000000 INFO @ Sun, 21 Jun 2020 21:01:34: 15000000 INFO @ Sun, 21 Jun 2020 21:01:35: 6000000 INFO @ Sun, 21 Jun 2020 21:01:37: 12000000 INFO @ Sun, 21 Jun 2020 21:01:40: 16000000 INFO @ Sun, 21 Jun 2020 21:01:41: 7000000 INFO @ Sun, 21 Jun 2020 21:01:43: 13000000 INFO @ Sun, 21 Jun 2020 21:01:46: 8000000 INFO @ Sun, 21 Jun 2020 21:01:46: 17000000 INFO @ Sun, 21 Jun 2020 21:01:48: 14000000 INFO @ Sun, 21 Jun 2020 21:01:49: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:01:49: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:01:49: #1 total tags in treatment: 17395072 INFO @ Sun, 21 Jun 2020 21:01:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:01:49: #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 21:01:49: #1 tags after filtering in treatment: 17395014 INFO @ Sun, 21 Jun 2020 21:01:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:01:49: #1 finished! INFO @ Sun, 21 Jun 2020 21:01:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:01:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:01:50: #2 number of paired peaks: 1691 INFO @ Sun, 21 Jun 2020 21:01:50: start model_add_line... INFO @ Sun, 21 Jun 2020 21:01:51: start X-correlation... INFO @ Sun, 21 Jun 2020 21:01:51: end of X-cor INFO @ Sun, 21 Jun 2020 21:01:51: #2 finished! INFO @ Sun, 21 Jun 2020 21:01:51: #2 predicted fragment length is 49 bps INFO @ Sun, 21 Jun 2020 21:01:51: #2 alternative fragment length(s) may be 2,49 bps INFO @ Sun, 21 Jun 2020 21:01:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4664641/SRX4664641.05_model.r WARNING @ Sun, 21 Jun 2020 21:01:51: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:01:51: #2 You may need to consider one of the other alternative d(s): 2,49 WARNING @ Sun, 21 Jun 2020 21:01:51: #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 21:01:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:01:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:01:51: 9000000 INFO @ Sun, 21 Jun 2020 21:01:54: 15000000 INFO @ Sun, 21 Jun 2020 21:01:57: 10000000 INFO @ Sun, 21 Jun 2020 21:01:59: 16000000 INFO @ Sun, 21 Jun 2020 21:02:02: 11000000 INFO @ Sun, 21 Jun 2020 21:02:04: 17000000 INFO @ Sun, 21 Jun 2020 21:02:07: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:02:07: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:02:07: #1 total tags in treatment: 17395072 INFO @ Sun, 21 Jun 2020 21:02:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:02:07: #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 21:02:07: #1 tags after filtering in treatment: 17395014 INFO @ Sun, 21 Jun 2020 21:02:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:02:07: #1 finished! INFO @ Sun, 21 Jun 2020 21:02:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:02:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:02:07: 12000000 INFO @ Sun, 21 Jun 2020 21:02:08: #2 number of paired peaks: 1691 INFO @ Sun, 21 Jun 2020 21:02:08: start model_add_line... INFO @ Sun, 21 Jun 2020 21:02:09: start X-correlation... INFO @ Sun, 21 Jun 2020 21:02:09: end of X-cor INFO @ Sun, 21 Jun 2020 21:02:09: #2 finished! INFO @ Sun, 21 Jun 2020 21:02:09: #2 predicted fragment length is 49 bps INFO @ Sun, 21 Jun 2020 21:02:09: #2 alternative fragment length(s) may be 2,49 bps INFO @ Sun, 21 Jun 2020 21:02:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4664641/SRX4664641.10_model.r WARNING @ Sun, 21 Jun 2020 21:02:09: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:02:09: #2 You may need to consider one of the other alternative d(s): 2,49 WARNING @ Sun, 21 Jun 2020 21:02:09: #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 21:02:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:02:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:02:12: 13000000 INFO @ Sun, 21 Jun 2020 21:02:17: 14000000 INFO @ Sun, 21 Jun 2020 21:02:23: 15000000 INFO @ Sun, 21 Jun 2020 21:02:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:02:28: 16000000 INFO @ Sun, 21 Jun 2020 21:02:32: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:02:35: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:02:35: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:02:35: #1 total tags in treatment: 17395072 INFO @ Sun, 21 Jun 2020 21:02:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:02:35: #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 21:02:35: #1 tags after filtering in treatment: 17395014 INFO @ Sun, 21 Jun 2020 21:02:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:02:35: #1 finished! INFO @ Sun, 21 Jun 2020 21:02:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:02:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:02:36: #2 number of paired peaks: 1691 INFO @ Sun, 21 Jun 2020 21:02:36: start model_add_line... INFO @ Sun, 21 Jun 2020 21:02:36: start X-correlation... INFO @ Sun, 21 Jun 2020 21:02:37: end of X-cor INFO @ Sun, 21 Jun 2020 21:02:37: #2 finished! INFO @ Sun, 21 Jun 2020 21:02:37: #2 predicted fragment length is 49 bps INFO @ Sun, 21 Jun 2020 21:02:37: #2 alternative fragment length(s) may be 2,49 bps INFO @ Sun, 21 Jun 2020 21:02:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4664641/SRX4664641.20_model.r WARNING @ Sun, 21 Jun 2020 21:02:37: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:02:37: #2 You may need to consider one of the other alternative d(s): 2,49 WARNING @ Sun, 21 Jun 2020 21:02:37: #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 21:02:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:02:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:02:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4664641/SRX4664641.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:02:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4664641/SRX4664641.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:02:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4664641/SRX4664641.05_summits.bed INFO @ Sun, 21 Jun 2020 21:02:39: Done! pass1 - making usageList (605 chroms): 2 millis pass2 - checking and writing primary data (4517 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:02:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:02:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4664641/SRX4664641.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:02:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4664641/SRX4664641.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:02:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4664641/SRX4664641.10_summits.bed INFO @ Sun, 21 Jun 2020 21:02:58: Done! pass1 - making usageList (521 chroms): 1 millis pass2 - checking and writing primary data (2874 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:03:09: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:03:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4664641/SRX4664641.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:03:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4664641/SRX4664641.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:03:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4664641/SRX4664641.20_summits.bed INFO @ Sun, 21 Jun 2020 21:03:25: Done! pass1 - making usageList (415 chroms): 1 millis pass2 - checking and writing primary data (1327 records, 4 fields): 13 millis CompletedMACS2peakCalling