Job ID = 6509082 SRX = SRX645125 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T15:11:28 prefetch.2.10.7: 1) Downloading 'SRR1505725'... 2020-06-26T15:11:28 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T15:16:32 prefetch.2.10.7: HTTPS download succeed 2020-06-26T15:16:32 prefetch.2.10.7: 1) 'SRR1505725' was downloaded successfully Read 25772765 spots for SRR1505725/SRR1505725.sra Written 25772765 spots for SRR1505725/SRR1505725.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:49 25772765 reads; of these: 25772765 (100.00%) were unpaired; of these: 14964987 (58.07%) aligned 0 times 8701590 (33.76%) aligned exactly 1 time 2106188 (8.17%) aligned >1 times 41.93% overall alignment rate Time searching: 00:08:50 Overall time: 00:08:50 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] 4756595 / 10807778 = 0.4401 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 @ Sat, 27 Jun 2020 00:31:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX645125/SRX645125.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX645125/SRX645125.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX645125/SRX645125.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX645125/SRX645125.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 @ Sat, 27 Jun 2020 00:31:32: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:31:32: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:31:40: 1000000 INFO @ Sat, 27 Jun 2020 00:31:48: 2000000 INFO @ Sat, 27 Jun 2020 00:31:55: 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 @ Sat, 27 Jun 2020 00:32:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX645125/SRX645125.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX645125/SRX645125.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX645125/SRX645125.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX645125/SRX645125.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 @ Sat, 27 Jun 2020 00:32:02: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:32:02: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:32:03: 4000000 INFO @ Sat, 27 Jun 2020 00:32:12: 1000000 INFO @ Sat, 27 Jun 2020 00:32:13: 5000000 INFO @ Sat, 27 Jun 2020 00:32:21: 2000000 INFO @ Sat, 27 Jun 2020 00:32:23: 6000000 INFO @ Sat, 27 Jun 2020 00:32:23: #1 tag size is determined as 100 bps INFO @ Sat, 27 Jun 2020 00:32:23: #1 tag size = 100 INFO @ Sat, 27 Jun 2020 00:32:23: #1 total tags in treatment: 6051183 INFO @ Sat, 27 Jun 2020 00:32:23: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:32:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:32:24: #1 tags after filtering in treatment: 6051151 INFO @ Sat, 27 Jun 2020 00:32:24: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:32:24: #1 finished! INFO @ Sat, 27 Jun 2020 00:32:24: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:32:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:32:24: #2 number of paired peaks: 1814 INFO @ Sat, 27 Jun 2020 00:32:24: start model_add_line... INFO @ Sat, 27 Jun 2020 00:32:24: start X-correlation... INFO @ Sat, 27 Jun 2020 00:32:24: end of X-cor INFO @ Sat, 27 Jun 2020 00:32:24: #2 finished! INFO @ Sat, 27 Jun 2020 00:32:24: #2 predicted fragment length is 126 bps INFO @ Sat, 27 Jun 2020 00:32:24: #2 alternative fragment length(s) may be 126 bps INFO @ Sat, 27 Jun 2020 00:32:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX645125/SRX645125.05_model.r WARNING @ Sat, 27 Jun 2020 00:32:24: #2 Since the d (126) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:32:24: #2 You may need to consider one of the other alternative d(s): 126 WARNING @ Sat, 27 Jun 2020 00:32:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:32:24: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:32:24: #3 Pre-compute pvalue-qvalue table... 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 @ Sat, 27 Jun 2020 00:32:30: 3000000 INFO @ Sat, 27 Jun 2020 00:32:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX645125/SRX645125.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX645125/SRX645125.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX645125/SRX645125.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX645125/SRX645125.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 @ Sat, 27 Jun 2020 00:32:32: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:32:32: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:32:40: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:32:40: 4000000 INFO @ Sat, 27 Jun 2020 00:32:43: 1000000 INFO @ Sat, 27 Jun 2020 00:32:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX645125/SRX645125.05_peaks.xls INFO @ Sat, 27 Jun 2020 00:32:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX645125/SRX645125.05_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:32:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX645125/SRX645125.05_summits.bed INFO @ Sat, 27 Jun 2020 00:32:48: Done! pass1 - making usageList (582 chroms): 1 millis pass2 - checking and writing primary data (4660 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:32:50: 5000000 INFO @ Sat, 27 Jun 2020 00:32:53: 2000000 INFO @ Sat, 27 Jun 2020 00:33:00: 6000000 INFO @ Sat, 27 Jun 2020 00:33:01: #1 tag size is determined as 100 bps INFO @ Sat, 27 Jun 2020 00:33:01: #1 tag size = 100 INFO @ Sat, 27 Jun 2020 00:33:01: #1 total tags in treatment: 6051183 INFO @ Sat, 27 Jun 2020 00:33:01: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:33:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:33:01: #1 tags after filtering in treatment: 6051151 INFO @ Sat, 27 Jun 2020 00:33:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:33:01: #1 finished! INFO @ Sat, 27 Jun 2020 00:33:01: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:33:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:33:02: #2 number of paired peaks: 1814 INFO @ Sat, 27 Jun 2020 00:33:02: start model_add_line... INFO @ Sat, 27 Jun 2020 00:33:02: start X-correlation... INFO @ Sat, 27 Jun 2020 00:33:02: end of X-cor INFO @ Sat, 27 Jun 2020 00:33:02: #2 finished! INFO @ Sat, 27 Jun 2020 00:33:02: #2 predicted fragment length is 126 bps INFO @ Sat, 27 Jun 2020 00:33:02: #2 alternative fragment length(s) may be 126 bps INFO @ Sat, 27 Jun 2020 00:33:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX645125/SRX645125.10_model.r WARNING @ Sat, 27 Jun 2020 00:33:02: #2 Since the d (126) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:33:02: #2 You may need to consider one of the other alternative d(s): 126 WARNING @ Sat, 27 Jun 2020 00:33:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:33:02: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:33:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:33:03: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 27 Jun 2020 00:33:13: 4000000 INFO @ Sat, 27 Jun 2020 00:33:19: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:33:26: 5000000 INFO @ Sat, 27 Jun 2020 00:33:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX645125/SRX645125.10_peaks.xls INFO @ Sat, 27 Jun 2020 00:33:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX645125/SRX645125.10_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:33:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX645125/SRX645125.10_summits.bed INFO @ Sat, 27 Jun 2020 00:33:27: Done! pass1 - making usageList (446 chroms): 1 millis pass2 - checking and writing primary data (3189 records, 4 fields): 17 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 27 Jun 2020 00:33:36: 6000000 INFO @ Sat, 27 Jun 2020 00:33:36: #1 tag size is determined as 100 bps INFO @ Sat, 27 Jun 2020 00:33:36: #1 tag size = 100 INFO @ Sat, 27 Jun 2020 00:33:36: #1 total tags in treatment: 6051183 INFO @ Sat, 27 Jun 2020 00:33:36: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:33:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:33:37: #1 tags after filtering in treatment: 6051151 INFO @ Sat, 27 Jun 2020 00:33:37: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:33:37: #1 finished! INFO @ Sat, 27 Jun 2020 00:33:37: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:33:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:33:37: #2 number of paired peaks: 1814 INFO @ Sat, 27 Jun 2020 00:33:37: start model_add_line... INFO @ Sat, 27 Jun 2020 00:33:37: start X-correlation... INFO @ Sat, 27 Jun 2020 00:33:37: end of X-cor INFO @ Sat, 27 Jun 2020 00:33:37: #2 finished! INFO @ Sat, 27 Jun 2020 00:33:37: #2 predicted fragment length is 126 bps INFO @ Sat, 27 Jun 2020 00:33:37: #2 alternative fragment length(s) may be 126 bps INFO @ Sat, 27 Jun 2020 00:33:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX645125/SRX645125.20_model.r WARNING @ Sat, 27 Jun 2020 00:33:37: #2 Since the d (126) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:33:37: #2 You may need to consider one of the other alternative d(s): 126 WARNING @ Sat, 27 Jun 2020 00:33:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:33:37: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:33:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:33:52: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:33:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX645125/SRX645125.20_peaks.xls INFO @ Sat, 27 Jun 2020 00:33:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX645125/SRX645125.20_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:33:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX645125/SRX645125.20_summits.bed INFO @ Sat, 27 Jun 2020 00:33:59: Done! pass1 - making usageList (287 chroms): 1 millis pass2 - checking and writing primary data (1635 records, 4 fields): 11 millis CompletedMACS2peakCalling