Job ID = 6454290 SRX = SRX197564 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:57:23 prefetch.2.10.7: 1) Downloading 'SRR596992'... 2020-06-21T08:57:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:03:44 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:03:44 prefetch.2.10.7: 1) 'SRR596992' was downloaded successfully Read 29732460 spots for SRR596992/SRR596992.sra Written 29732460 spots for SRR596992/SRR596992.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: 00:07:21 29732460 reads; of these: 29732460 (100.00%) were unpaired; of these: 5427293 (18.25%) aligned 0 times 16708001 (56.19%) aligned exactly 1 time 7597166 (25.55%) aligned >1 times 81.75% overall alignment rate Time searching: 00:07:21 Overall time: 00:07:21 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] 9959345 / 24305167 = 0.4098 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 18:17:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX197564/SRX197564.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX197564/SRX197564.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX197564/SRX197564.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX197564/SRX197564.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 18:17:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:17:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:17:58: 1000000 INFO @ Sun, 21 Jun 2020 18:18:04: 2000000 INFO @ Sun, 21 Jun 2020 18:18:10: 3000000 INFO @ Sun, 21 Jun 2020 18:18:15: 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 18:18:21: 5000000 INFO @ Sun, 21 Jun 2020 18:18:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX197564/SRX197564.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX197564/SRX197564.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX197564/SRX197564.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX197564/SRX197564.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 18:18:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:18:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:18:27: 6000000 INFO @ Sun, 21 Jun 2020 18:18:29: 1000000 INFO @ Sun, 21 Jun 2020 18:18:34: 7000000 INFO @ Sun, 21 Jun 2020 18:18:35: 2000000 INFO @ Sun, 21 Jun 2020 18:18:40: 8000000 INFO @ Sun, 21 Jun 2020 18:18:41: 3000000 INFO @ Sun, 21 Jun 2020 18:18:46: 9000000 INFO @ Sun, 21 Jun 2020 18:18:47: 4000000 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 18:18:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX197564/SRX197564.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX197564/SRX197564.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX197564/SRX197564.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX197564/SRX197564.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 18:18:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:18:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:18:53: 10000000 INFO @ Sun, 21 Jun 2020 18:18:54: 5000000 INFO @ Sun, 21 Jun 2020 18:18:58: 1000000 INFO @ Sun, 21 Jun 2020 18:18:59: 11000000 INFO @ Sun, 21 Jun 2020 18:19:00: 6000000 INFO @ Sun, 21 Jun 2020 18:19:04: 2000000 INFO @ Sun, 21 Jun 2020 18:19:06: 12000000 INFO @ Sun, 21 Jun 2020 18:19:07: 7000000 INFO @ Sun, 21 Jun 2020 18:19:10: 3000000 INFO @ Sun, 21 Jun 2020 18:19:13: 13000000 INFO @ Sun, 21 Jun 2020 18:19:14: 8000000 INFO @ Sun, 21 Jun 2020 18:19:15: 4000000 INFO @ Sun, 21 Jun 2020 18:19:20: 14000000 INFO @ Sun, 21 Jun 2020 18:19:21: 9000000 INFO @ Sun, 21 Jun 2020 18:19:22: 5000000 INFO @ Sun, 21 Jun 2020 18:19:23: #1 tag size is determined as 45 bps INFO @ Sun, 21 Jun 2020 18:19:23: #1 tag size = 45 INFO @ Sun, 21 Jun 2020 18:19:23: #1 total tags in treatment: 14345822 INFO @ Sun, 21 Jun 2020 18:19:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:19:23: #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 18:19:23: #1 tags after filtering in treatment: 14345822 INFO @ Sun, 21 Jun 2020 18:19:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:19:23: #1 finished! INFO @ Sun, 21 Jun 2020 18:19:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:19:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:19:24: #2 number of paired peaks: 1053 INFO @ Sun, 21 Jun 2020 18:19:24: start model_add_line... INFO @ Sun, 21 Jun 2020 18:19:25: start X-correlation... INFO @ Sun, 21 Jun 2020 18:19:25: end of X-cor INFO @ Sun, 21 Jun 2020 18:19:25: #2 finished! INFO @ Sun, 21 Jun 2020 18:19:25: #2 predicted fragment length is 37 bps INFO @ Sun, 21 Jun 2020 18:19:25: #2 alternative fragment length(s) may be 2,37 bps INFO @ Sun, 21 Jun 2020 18:19:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX197564/SRX197564.05_model.r WARNING @ Sun, 21 Jun 2020 18:19:25: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:19:25: #2 You may need to consider one of the other alternative d(s): 2,37 WARNING @ Sun, 21 Jun 2020 18:19:25: #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 18:19:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:19:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:19:27: 6000000 INFO @ Sun, 21 Jun 2020 18:19:28: 10000000 INFO @ Sun, 21 Jun 2020 18:19:33: 7000000 INFO @ Sun, 21 Jun 2020 18:19:35: 11000000 INFO @ Sun, 21 Jun 2020 18:19:39: 8000000 INFO @ Sun, 21 Jun 2020 18:19:42: 12000000 INFO @ Sun, 21 Jun 2020 18:19:45: 9000000 INFO @ Sun, 21 Jun 2020 18:19:49: 13000000 INFO @ Sun, 21 Jun 2020 18:19:51: 10000000 INFO @ Sun, 21 Jun 2020 18:19:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:19:56: 14000000 INFO @ Sun, 21 Jun 2020 18:19:57: 11000000 INFO @ Sun, 21 Jun 2020 18:19:59: #1 tag size is determined as 45 bps INFO @ Sun, 21 Jun 2020 18:19:59: #1 tag size = 45 INFO @ Sun, 21 Jun 2020 18:19:59: #1 total tags in treatment: 14345822 INFO @ Sun, 21 Jun 2020 18:19:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:19:59: #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 18:19:59: #1 tags after filtering in treatment: 14345822 INFO @ Sun, 21 Jun 2020 18:19:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:19:59: #1 finished! INFO @ Sun, 21 Jun 2020 18:19:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:19:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:20:01: #2 number of paired peaks: 1053 INFO @ Sun, 21 Jun 2020 18:20:01: start model_add_line... INFO @ Sun, 21 Jun 2020 18:20:01: start X-correlation... INFO @ Sun, 21 Jun 2020 18:20:01: end of X-cor INFO @ Sun, 21 Jun 2020 18:20:01: #2 finished! INFO @ Sun, 21 Jun 2020 18:20:01: #2 predicted fragment length is 37 bps INFO @ Sun, 21 Jun 2020 18:20:01: #2 alternative fragment length(s) may be 2,37 bps INFO @ Sun, 21 Jun 2020 18:20:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX197564/SRX197564.10_model.r WARNING @ Sun, 21 Jun 2020 18:20:01: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:20:01: #2 You may need to consider one of the other alternative d(s): 2,37 WARNING @ Sun, 21 Jun 2020 18:20:01: #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 18:20:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:20:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:20:03: 12000000 INFO @ Sun, 21 Jun 2020 18:20:08: 13000000 INFO @ Sun, 21 Jun 2020 18:20:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX197564/SRX197564.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:20:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX197564/SRX197564.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:20:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX197564/SRX197564.05_summits.bed INFO @ Sun, 21 Jun 2020 18:20:10: Done! pass1 - making usageList (708 chroms): 2 millis pass2 - checking and writing primary data (3095 records, 4 fields): 24 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:20:14: 14000000 INFO @ Sun, 21 Jun 2020 18:20:16: #1 tag size is determined as 45 bps INFO @ Sun, 21 Jun 2020 18:20:16: #1 tag size = 45 INFO @ Sun, 21 Jun 2020 18:20:16: #1 total tags in treatment: 14345822 INFO @ Sun, 21 Jun 2020 18:20:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:20:16: #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 18:20:17: #1 tags after filtering in treatment: 14345822 INFO @ Sun, 21 Jun 2020 18:20:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:20:17: #1 finished! INFO @ Sun, 21 Jun 2020 18:20:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:20:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:20:18: #2 number of paired peaks: 1053 INFO @ Sun, 21 Jun 2020 18:20:18: start model_add_line... INFO @ Sun, 21 Jun 2020 18:20:18: start X-correlation... INFO @ Sun, 21 Jun 2020 18:20:18: end of X-cor INFO @ Sun, 21 Jun 2020 18:20:18: #2 finished! INFO @ Sun, 21 Jun 2020 18:20:18: #2 predicted fragment length is 37 bps INFO @ Sun, 21 Jun 2020 18:20:18: #2 alternative fragment length(s) may be 2,37 bps INFO @ Sun, 21 Jun 2020 18:20:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX197564/SRX197564.20_model.r WARNING @ Sun, 21 Jun 2020 18:20:18: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:20:18: #2 You may need to consider one of the other alternative d(s): 2,37 WARNING @ Sun, 21 Jun 2020 18:20:18: #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 18:20:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:20:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:20:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:20:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:20:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX197564/SRX197564.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:20:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX197564/SRX197564.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:20:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX197564/SRX197564.10_summits.bed INFO @ Sun, 21 Jun 2020 18:20:47: Done! BigWig に変換しました。 pass1 - making usageList (600 chroms): 1 millis pass2 - checking and writing primary data (2401 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:21:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX197564/SRX197564.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:21:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX197564/SRX197564.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:21:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX197564/SRX197564.20_summits.bed INFO @ Sun, 21 Jun 2020 18:21:01: Done! pass1 - making usageList (410 chroms): 1 millis pass2 - checking and writing primary data (1318 records, 4 fields): 13 millis CompletedMACS2peakCalling