Job ID = 6453844 SRX = SRX152099 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:35:09 prefetch.2.10.7: 1) Downloading 'SRR504955'... 2020-06-21T08:35:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:38:40 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:38:40 prefetch.2.10.7: 1) 'SRR504955' was downloaded successfully Read 26375444 spots for SRR504955/SRR504955.sra Written 26375444 spots for SRR504955/SRR504955.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: 00:12:45 26375444 reads; of these: 26375444 (100.00%) were unpaired; of these: 3079058 (11.67%) aligned 0 times 12401009 (47.02%) aligned exactly 1 time 10895377 (41.31%) aligned >1 times 88.33% overall alignment rate Time searching: 00:12:45 Overall time: 00:12:45 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] 12004407 / 23296386 = 0.5153 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 17:57:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX152099/SRX152099.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX152099/SRX152099.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX152099/SRX152099.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX152099/SRX152099.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 17:57:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:57:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:57:43: 1000000 INFO @ Sun, 21 Jun 2020 17:57:48: 2000000 INFO @ Sun, 21 Jun 2020 17:57:54: 3000000 INFO @ Sun, 21 Jun 2020 17:57:59: 4000000 INFO @ Sun, 21 Jun 2020 17:58:04: 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 17:58:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX152099/SRX152099.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX152099/SRX152099.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX152099/SRX152099.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX152099/SRX152099.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 17:58:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:58:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:58:09: 6000000 INFO @ Sun, 21 Jun 2020 17:58:15: 1000000 INFO @ Sun, 21 Jun 2020 17:58:15: 7000000 INFO @ Sun, 21 Jun 2020 17:58:20: 2000000 INFO @ Sun, 21 Jun 2020 17:58:20: 8000000 INFO @ Sun, 21 Jun 2020 17:58:26: 3000000 INFO @ Sun, 21 Jun 2020 17:58:26: 9000000 INFO @ Sun, 21 Jun 2020 17:58:32: 4000000 INFO @ Sun, 21 Jun 2020 17:58:32: 10000000 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 17:58:37: 5000000 INFO @ Sun, 21 Jun 2020 17:58:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX152099/SRX152099.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX152099/SRX152099.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX152099/SRX152099.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX152099/SRX152099.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 17:58:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:58:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:58:38: 11000000 INFO @ Sun, 21 Jun 2020 17:58:40: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:58:40: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:58:40: #1 total tags in treatment: 11291979 INFO @ Sun, 21 Jun 2020 17:58:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:58:40: #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 17:58:40: #1 tags after filtering in treatment: 11291972 INFO @ Sun, 21 Jun 2020 17:58:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:58:40: #1 finished! INFO @ Sun, 21 Jun 2020 17:58:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:58:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:58:41: #2 number of paired peaks: 2404 INFO @ Sun, 21 Jun 2020 17:58:41: start model_add_line... INFO @ Sun, 21 Jun 2020 17:58:41: start X-correlation... INFO @ Sun, 21 Jun 2020 17:58:41: end of X-cor INFO @ Sun, 21 Jun 2020 17:58:41: #2 finished! INFO @ Sun, 21 Jun 2020 17:58:41: #2 predicted fragment length is 40 bps INFO @ Sun, 21 Jun 2020 17:58:41: #2 alternative fragment length(s) may be 4,40 bps INFO @ Sun, 21 Jun 2020 17:58:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX152099/SRX152099.05_model.r WARNING @ Sun, 21 Jun 2020 17:58:41: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:58:41: #2 You may need to consider one of the other alternative d(s): 4,40 WARNING @ Sun, 21 Jun 2020 17:58:41: #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 17:58:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:58:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:58:43: 6000000 INFO @ Sun, 21 Jun 2020 17:58:44: 1000000 INFO @ Sun, 21 Jun 2020 17:58:49: 7000000 INFO @ Sun, 21 Jun 2020 17:58:51: 2000000 INFO @ Sun, 21 Jun 2020 17:58:55: 8000000 INFO @ Sun, 21 Jun 2020 17:58:57: 3000000 INFO @ Sun, 21 Jun 2020 17:59:01: 9000000 INFO @ Sun, 21 Jun 2020 17:59:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:59:04: 4000000 INFO @ Sun, 21 Jun 2020 17:59:07: 10000000 INFO @ Sun, 21 Jun 2020 17:59:10: 5000000 INFO @ Sun, 21 Jun 2020 17:59:13: 11000000 INFO @ Sun, 21 Jun 2020 17:59:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX152099/SRX152099.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:59:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX152099/SRX152099.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:59:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX152099/SRX152099.05_summits.bed INFO @ Sun, 21 Jun 2020 17:59:14: Done! pass1 - making usageList (663 chroms): 2 millis pass2 - checking and writing primary data (7026 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:59:15: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:59:15: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:59:15: #1 total tags in treatment: 11291979 INFO @ Sun, 21 Jun 2020 17:59:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:59:15: #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 17:59:15: #1 tags after filtering in treatment: 11291972 INFO @ Sun, 21 Jun 2020 17:59:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:59:15: #1 finished! INFO @ Sun, 21 Jun 2020 17:59:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:59:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:59:16: 6000000 INFO @ Sun, 21 Jun 2020 17:59:16: #2 number of paired peaks: 2404 INFO @ Sun, 21 Jun 2020 17:59:16: start model_add_line... INFO @ Sun, 21 Jun 2020 17:59:17: start X-correlation... INFO @ Sun, 21 Jun 2020 17:59:17: end of X-cor INFO @ Sun, 21 Jun 2020 17:59:17: #2 finished! INFO @ Sun, 21 Jun 2020 17:59:17: #2 predicted fragment length is 40 bps INFO @ Sun, 21 Jun 2020 17:59:17: #2 alternative fragment length(s) may be 4,40 bps INFO @ Sun, 21 Jun 2020 17:59:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX152099/SRX152099.10_model.r WARNING @ Sun, 21 Jun 2020 17:59:17: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:59:17: #2 You may need to consider one of the other alternative d(s): 4,40 WARNING @ Sun, 21 Jun 2020 17:59:17: #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 17:59:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:59:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:59:23: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:59:29: 8000000 INFO @ Sun, 21 Jun 2020 17:59:35: 9000000 INFO @ Sun, 21 Jun 2020 17:59:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:59:41: 10000000 INFO @ Sun, 21 Jun 2020 17:59:47: 11000000 INFO @ Sun, 21 Jun 2020 17:59:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX152099/SRX152099.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:59:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX152099/SRX152099.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:59:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX152099/SRX152099.10_summits.bed INFO @ Sun, 21 Jun 2020 17:59:49: Done! INFO @ Sun, 21 Jun 2020 17:59:49: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:59:49: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:59:49: #1 total tags in treatment: 11291979 INFO @ Sun, 21 Jun 2020 17:59:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:59:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (476 chroms): 2 millis pass2 - checking and writing primary data (4058 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:59:49: #1 tags after filtering in treatment: 11291972 INFO @ Sun, 21 Jun 2020 17:59:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:59:49: #1 finished! INFO @ Sun, 21 Jun 2020 17:59:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:59:49: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:59:50: #2 number of paired peaks: 2404 INFO @ Sun, 21 Jun 2020 17:59:50: start model_add_line... INFO @ Sun, 21 Jun 2020 17:59:51: start X-correlation... INFO @ Sun, 21 Jun 2020 17:59:51: end of X-cor INFO @ Sun, 21 Jun 2020 17:59:51: #2 finished! INFO @ Sun, 21 Jun 2020 17:59:51: #2 predicted fragment length is 40 bps INFO @ Sun, 21 Jun 2020 17:59:51: #2 alternative fragment length(s) may be 4,40 bps INFO @ Sun, 21 Jun 2020 17:59:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX152099/SRX152099.20_model.r WARNING @ Sun, 21 Jun 2020 17:59:51: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:59:51: #2 You may need to consider one of the other alternative d(s): 4,40 WARNING @ Sun, 21 Jun 2020 17:59:51: #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 17:59:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:59:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:00:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:00:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX152099/SRX152099.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:00:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX152099/SRX152099.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:00:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX152099/SRX152099.20_summits.bed INFO @ Sun, 21 Jun 2020 18:00:24: Done! pass1 - making usageList (270 chroms): 1 millis pass2 - checking and writing primary data (776 records, 4 fields): 9 millis CompletedMACS2peakCalling