Job ID = 6527856 SRX = SRX287882 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T13:50:04 prefetch.2.10.7: 1) Downloading 'SRR870071'... 2020-06-29T13:50:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:53:01 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:53:01 prefetch.2.10.7: 1) 'SRR870071' was downloaded successfully Read 26274958 spots for SRR870071/SRR870071.sra Written 26274958 spots for SRR870071/SRR870071.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: 00:09:54 26274958 reads; of these: 26274958 (100.00%) were unpaired; of these: 1296628 (4.93%) aligned 0 times 16585644 (63.12%) aligned exactly 1 time 8392686 (31.94%) aligned >1 times 95.07% overall alignment rate Time searching: 00:09:54 Overall time: 00:09:54 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] 4734200 / 24978330 = 0.1895 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 @ Mon, 29 Jun 2020 23:15:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287882/SRX287882.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287882/SRX287882.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287882/SRX287882.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287882/SRX287882.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 @ Mon, 29 Jun 2020 23:15:58: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:15:58: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:16:04: 1000000 INFO @ Mon, 29 Jun 2020 23:16:09: 2000000 INFO @ Mon, 29 Jun 2020 23:16:14: 3000000 INFO @ Mon, 29 Jun 2020 23:16:20: 4000000 INFO @ Mon, 29 Jun 2020 23:16:25: 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 @ Mon, 29 Jun 2020 23:16:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287882/SRX287882.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287882/SRX287882.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287882/SRX287882.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287882/SRX287882.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 @ Mon, 29 Jun 2020 23:16:28: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:16:28: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:16:31: 6000000 INFO @ Mon, 29 Jun 2020 23:16:34: 1000000 INFO @ Mon, 29 Jun 2020 23:16:37: 7000000 INFO @ Mon, 29 Jun 2020 23:16:40: 2000000 INFO @ Mon, 29 Jun 2020 23:16:43: 8000000 INFO @ Mon, 29 Jun 2020 23:16:46: 3000000 INFO @ Mon, 29 Jun 2020 23:16:49: 9000000 INFO @ Mon, 29 Jun 2020 23:16:53: 4000000 INFO @ Mon, 29 Jun 2020 23:16:55: 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 @ Mon, 29 Jun 2020 23:16:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287882/SRX287882.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287882/SRX287882.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287882/SRX287882.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287882/SRX287882.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 @ Mon, 29 Jun 2020 23:16:58: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:16:58: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:16:59: 5000000 INFO @ Mon, 29 Jun 2020 23:17:01: 11000000 INFO @ Mon, 29 Jun 2020 23:17:04: 1000000 INFO @ Mon, 29 Jun 2020 23:17:05: 6000000 INFO @ Mon, 29 Jun 2020 23:17:07: 12000000 INFO @ Mon, 29 Jun 2020 23:17:11: 2000000 INFO @ Mon, 29 Jun 2020 23:17:11: 7000000 INFO @ Mon, 29 Jun 2020 23:17:14: 13000000 INFO @ Mon, 29 Jun 2020 23:17:17: 3000000 INFO @ Mon, 29 Jun 2020 23:17:17: 8000000 INFO @ Mon, 29 Jun 2020 23:17:20: 14000000 INFO @ Mon, 29 Jun 2020 23:17:23: 4000000 INFO @ Mon, 29 Jun 2020 23:17:24: 9000000 INFO @ Mon, 29 Jun 2020 23:17:26: 15000000 INFO @ Mon, 29 Jun 2020 23:17:29: 5000000 INFO @ Mon, 29 Jun 2020 23:17:30: 10000000 INFO @ Mon, 29 Jun 2020 23:17:32: 16000000 INFO @ Mon, 29 Jun 2020 23:17:35: 6000000 INFO @ Mon, 29 Jun 2020 23:17:36: 11000000 INFO @ Mon, 29 Jun 2020 23:17:38: 17000000 INFO @ Mon, 29 Jun 2020 23:17:41: 7000000 INFO @ Mon, 29 Jun 2020 23:17:42: 12000000 INFO @ Mon, 29 Jun 2020 23:17:44: 18000000 INFO @ Mon, 29 Jun 2020 23:17:47: 8000000 INFO @ Mon, 29 Jun 2020 23:17:48: 13000000 INFO @ Mon, 29 Jun 2020 23:17:51: 19000000 INFO @ Mon, 29 Jun 2020 23:17:53: 9000000 INFO @ Mon, 29 Jun 2020 23:17:55: 14000000 INFO @ Mon, 29 Jun 2020 23:17:57: 20000000 INFO @ Mon, 29 Jun 2020 23:17:58: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:17:58: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:17:58: #1 total tags in treatment: 20244130 INFO @ Mon, 29 Jun 2020 23:17:58: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:17:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:17:59: #1 tags after filtering in treatment: 20244130 INFO @ Mon, 29 Jun 2020 23:17:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:17:59: #1 finished! INFO @ Mon, 29 Jun 2020 23:17:59: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:17:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:18:00: 10000000 INFO @ Mon, 29 Jun 2020 23:18:00: #2 number of paired peaks: 190 WARNING @ Mon, 29 Jun 2020 23:18:00: Fewer paired peaks (190) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 190 pairs to build model! INFO @ Mon, 29 Jun 2020 23:18:00: start model_add_line... INFO @ Mon, 29 Jun 2020 23:18:00: start X-correlation... INFO @ Mon, 29 Jun 2020 23:18:00: end of X-cor INFO @ Mon, 29 Jun 2020 23:18:00: #2 finished! INFO @ Mon, 29 Jun 2020 23:18:00: #2 predicted fragment length is 45 bps INFO @ Mon, 29 Jun 2020 23:18:00: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 29 Jun 2020 23:18:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287882/SRX287882.05_model.r WARNING @ Mon, 29 Jun 2020 23:18:00: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:18:00: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 29 Jun 2020 23:18:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:18:00: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:18:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:18:01: 15000000 INFO @ Mon, 29 Jun 2020 23:18:06: 11000000 INFO @ Mon, 29 Jun 2020 23:18:07: 16000000 INFO @ Mon, 29 Jun 2020 23:18:12: 12000000 INFO @ Mon, 29 Jun 2020 23:18:13: 17000000 INFO @ Mon, 29 Jun 2020 23:18:18: 13000000 INFO @ Mon, 29 Jun 2020 23:18:19: 18000000 INFO @ Mon, 29 Jun 2020 23:18:24: 14000000 INFO @ Mon, 29 Jun 2020 23:18:25: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:18:30: 15000000 INFO @ Mon, 29 Jun 2020 23:18:31: 20000000 INFO @ Mon, 29 Jun 2020 23:18:33: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:18:33: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:18:33: #1 total tags in treatment: 20244130 INFO @ Mon, 29 Jun 2020 23:18:33: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:18:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:18:33: #1 tags after filtering in treatment: 20244130 INFO @ Mon, 29 Jun 2020 23:18:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:18:33: #1 finished! INFO @ Mon, 29 Jun 2020 23:18:33: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:18:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:18:34: #2 number of paired peaks: 190 WARNING @ Mon, 29 Jun 2020 23:18:34: Fewer paired peaks (190) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 190 pairs to build model! INFO @ Mon, 29 Jun 2020 23:18:34: start model_add_line... INFO @ Mon, 29 Jun 2020 23:18:34: start X-correlation... INFO @ Mon, 29 Jun 2020 23:18:34: end of X-cor INFO @ Mon, 29 Jun 2020 23:18:34: #2 finished! INFO @ Mon, 29 Jun 2020 23:18:34: #2 predicted fragment length is 45 bps INFO @ Mon, 29 Jun 2020 23:18:34: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 29 Jun 2020 23:18:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287882/SRX287882.10_model.r WARNING @ Mon, 29 Jun 2020 23:18:34: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:18:34: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 29 Jun 2020 23:18:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:18:34: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:18:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:18:36: 16000000 INFO @ Mon, 29 Jun 2020 23:18:36: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:18:41: 17000000 INFO @ Mon, 29 Jun 2020 23:18:46: 18000000 INFO @ Mon, 29 Jun 2020 23:18:52: 19000000 INFO @ Mon, 29 Jun 2020 23:18:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287882/SRX287882.05_peaks.xls INFO @ Mon, 29 Jun 2020 23:18:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287882/SRX287882.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:18:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287882/SRX287882.05_summits.bed INFO @ Mon, 29 Jun 2020 23:18:55: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2274 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:18:57: 20000000 INFO @ Mon, 29 Jun 2020 23:18:59: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:18:59: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:18:59: #1 total tags in treatment: 20244130 INFO @ Mon, 29 Jun 2020 23:18:59: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:18:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:18:59: #1 tags after filtering in treatment: 20244130 INFO @ Mon, 29 Jun 2020 23:18:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:18:59: #1 finished! INFO @ Mon, 29 Jun 2020 23:18:59: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:18:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:19:00: #2 number of paired peaks: 190 WARNING @ Mon, 29 Jun 2020 23:19:00: Fewer paired peaks (190) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 190 pairs to build model! INFO @ Mon, 29 Jun 2020 23:19:00: start model_add_line... INFO @ Mon, 29 Jun 2020 23:19:00: start X-correlation... INFO @ Mon, 29 Jun 2020 23:19:00: end of X-cor INFO @ Mon, 29 Jun 2020 23:19:00: #2 finished! INFO @ Mon, 29 Jun 2020 23:19:00: #2 predicted fragment length is 45 bps INFO @ Mon, 29 Jun 2020 23:19:00: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 29 Jun 2020 23:19:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287882/SRX287882.20_model.r WARNING @ Mon, 29 Jun 2020 23:19:00: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:19:00: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 29 Jun 2020 23:19:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:19:00: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:19:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:19:11: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 23:19:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287882/SRX287882.10_peaks.xls INFO @ Mon, 29 Jun 2020 23:19:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287882/SRX287882.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:19:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287882/SRX287882.10_summits.bed INFO @ Mon, 29 Jun 2020 23:19:29: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1872 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:19:36: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:19:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287882/SRX287882.20_peaks.xls INFO @ Mon, 29 Jun 2020 23:19:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287882/SRX287882.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:19:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287882/SRX287882.20_summits.bed INFO @ Mon, 29 Jun 2020 23:19:55: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1427 records, 4 fields): 3 millis CompletedMACS2peakCalling