Job ID = 6457829 SRX = SRX4798871 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:53:18 prefetch.2.10.7: 1) Downloading 'SRR7965198'... 2020-06-21T11:53:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:56:47 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:56:47 prefetch.2.10.7: 1) 'SRR7965198' was downloaded successfully Read 14991244 spots for SRR7965198/SRR7965198.sra Written 14991244 spots for SRR7965198/SRR7965198.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: 00:03:15 14991244 reads; of these: 14991244 (100.00%) were unpaired; of these: 2484417 (16.57%) aligned 0 times 11001019 (73.38%) aligned exactly 1 time 1505808 (10.04%) aligned >1 times 83.43% overall alignment rate Time searching: 00:03:15 Overall time: 00:03:15 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] 4138066 / 12506827 = 0.3309 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 21:04:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4798871/SRX4798871.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4798871/SRX4798871.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4798871/SRX4798871.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4798871/SRX4798871.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 21:04:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:04:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:04:19: 1000000 INFO @ Sun, 21 Jun 2020 21:04:25: 2000000 INFO @ Sun, 21 Jun 2020 21:04:30: 3000000 INFO @ Sun, 21 Jun 2020 21:04:36: 4000000 INFO @ Sun, 21 Jun 2020 21:04:42: 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 21:04:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4798871/SRX4798871.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4798871/SRX4798871.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4798871/SRX4798871.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4798871/SRX4798871.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 21:04:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:04:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:04:47: 6000000 INFO @ Sun, 21 Jun 2020 21:04:48: 1000000 INFO @ Sun, 21 Jun 2020 21:04:53: 7000000 INFO @ Sun, 21 Jun 2020 21:04:53: 2000000 INFO @ Sun, 21 Jun 2020 21:04:58: 3000000 INFO @ Sun, 21 Jun 2020 21:04:59: 8000000 INFO @ Sun, 21 Jun 2020 21:05:01: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:05:01: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:05:01: #1 total tags in treatment: 8368761 INFO @ Sun, 21 Jun 2020 21:05:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:05:01: #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 21:05:02: #1 tags after filtering in treatment: 8368709 INFO @ Sun, 21 Jun 2020 21:05:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:05:02: #1 finished! INFO @ Sun, 21 Jun 2020 21:05:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:05:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:05:02: #2 number of paired peaks: 253 WARNING @ Sun, 21 Jun 2020 21:05:02: Fewer paired peaks (253) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 253 pairs to build model! INFO @ Sun, 21 Jun 2020 21:05:02: start model_add_line... INFO @ Sun, 21 Jun 2020 21:05:02: start X-correlation... INFO @ Sun, 21 Jun 2020 21:05:02: end of X-cor INFO @ Sun, 21 Jun 2020 21:05:02: #2 finished! INFO @ Sun, 21 Jun 2020 21:05:02: #2 predicted fragment length is 146 bps INFO @ Sun, 21 Jun 2020 21:05:02: #2 alternative fragment length(s) may be 146 bps INFO @ Sun, 21 Jun 2020 21:05:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4798871/SRX4798871.05_model.r INFO @ Sun, 21 Jun 2020 21:05:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:05:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:05:03: 4000000 INFO @ Sun, 21 Jun 2020 21:05:08: 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 21:05:13: 6000000 INFO @ Sun, 21 Jun 2020 21:05:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4798871/SRX4798871.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4798871/SRX4798871.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4798871/SRX4798871.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4798871/SRX4798871.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 21:05:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:05:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:05:18: 7000000 INFO @ Sun, 21 Jun 2020 21:05:18: 1000000 INFO @ Sun, 21 Jun 2020 21:05:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:05:23: 8000000 INFO @ Sun, 21 Jun 2020 21:05:23: 2000000 INFO @ Sun, 21 Jun 2020 21:05:25: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:05:25: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:05:25: #1 total tags in treatment: 8368761 INFO @ Sun, 21 Jun 2020 21:05:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:05:25: #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 21:05:25: #1 tags after filtering in treatment: 8368709 INFO @ Sun, 21 Jun 2020 21:05:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:05:25: #1 finished! INFO @ Sun, 21 Jun 2020 21:05:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:05:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:05:26: #2 number of paired peaks: 253 WARNING @ Sun, 21 Jun 2020 21:05:26: Fewer paired peaks (253) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 253 pairs to build model! INFO @ Sun, 21 Jun 2020 21:05:26: start model_add_line... INFO @ Sun, 21 Jun 2020 21:05:26: start X-correlation... INFO @ Sun, 21 Jun 2020 21:05:26: end of X-cor INFO @ Sun, 21 Jun 2020 21:05:26: #2 finished! INFO @ Sun, 21 Jun 2020 21:05:26: #2 predicted fragment length is 146 bps INFO @ Sun, 21 Jun 2020 21:05:26: #2 alternative fragment length(s) may be 146 bps INFO @ Sun, 21 Jun 2020 21:05:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4798871/SRX4798871.10_model.r INFO @ Sun, 21 Jun 2020 21:05:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:05:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:05:28: 3000000 INFO @ Sun, 21 Jun 2020 21:05:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4798871/SRX4798871.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:05:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4798871/SRX4798871.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:05:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4798871/SRX4798871.05_summits.bed INFO @ Sun, 21 Jun 2020 21:05:29: Done! pass1 - making usageList (103 chroms): 1 millis pass2 - checking and writing primary data (353 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:05:33: 4000000 INFO @ Sun, 21 Jun 2020 21:05:38: 5000000 INFO @ Sun, 21 Jun 2020 21:05:43: 6000000 INFO @ Sun, 21 Jun 2020 21:05:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:05:48: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:05:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4798871/SRX4798871.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:05:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4798871/SRX4798871.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:05:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4798871/SRX4798871.10_summits.bed INFO @ Sun, 21 Jun 2020 21:05:52: Done! pass1 - making usageList (76 chroms): 0 millis pass2 - checking and writing primary data (151 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:05:53: 8000000 INFO @ Sun, 21 Jun 2020 21:05:55: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:05:55: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:05:55: #1 total tags in treatment: 8368761 INFO @ Sun, 21 Jun 2020 21:05:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:05:55: #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 21:05:55: #1 tags after filtering in treatment: 8368709 INFO @ Sun, 21 Jun 2020 21:05:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:05:55: #1 finished! INFO @ Sun, 21 Jun 2020 21:05:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:05:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:05:56: #2 number of paired peaks: 253 WARNING @ Sun, 21 Jun 2020 21:05:56: Fewer paired peaks (253) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 253 pairs to build model! INFO @ Sun, 21 Jun 2020 21:05:56: start model_add_line... INFO @ Sun, 21 Jun 2020 21:05:56: start X-correlation... INFO @ Sun, 21 Jun 2020 21:05:56: end of X-cor INFO @ Sun, 21 Jun 2020 21:05:56: #2 finished! INFO @ Sun, 21 Jun 2020 21:05:56: #2 predicted fragment length is 146 bps INFO @ Sun, 21 Jun 2020 21:05:56: #2 alternative fragment length(s) may be 146 bps INFO @ Sun, 21 Jun 2020 21:05:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4798871/SRX4798871.20_model.r INFO @ Sun, 21 Jun 2020 21:05:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:05:56: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:06:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:06:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4798871/SRX4798871.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:06:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4798871/SRX4798871.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:06:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4798871/SRX4798871.20_summits.bed INFO @ Sun, 21 Jun 2020 21:06:22: Done! pass1 - making usageList (50 chroms): 1 millis pass2 - checking and writing primary data (80 records, 4 fields): 5 millis CompletedMACS2peakCalling