Job ID = 6453727 SRX = SRX1433369 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:40:47 prefetch.2.10.7: 1) Downloading 'SRR2919834'... 2020-06-21T08:40:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:46:11 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:46:11 prefetch.2.10.7: 1) 'SRR2919834' was downloaded successfully Read 38591050 spots for SRR2919834/SRR2919834.sra Written 38591050 spots for SRR2919834/SRR2919834.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: 00:07:54 38591050 reads; of these: 38591050 (100.00%) were unpaired; of these: 18998899 (49.23%) aligned 0 times 14650419 (37.96%) aligned exactly 1 time 4941732 (12.81%) aligned >1 times 50.77% overall alignment rate Time searching: 00:07:54 Overall time: 00:07:54 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 6795444 / 19592151 = 0.3468 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 17:59:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433369/SRX1433369.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433369/SRX1433369.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433369/SRX1433369.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433369/SRX1433369.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 17:59:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:59:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:00:05: 1000000 INFO @ Sun, 21 Jun 2020 18:00:10: 2000000 INFO @ Sun, 21 Jun 2020 18:00:16: 3000000 INFO @ Sun, 21 Jun 2020 18:00:22: 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 18:00:27: 5000000 INFO @ Sun, 21 Jun 2020 18:00:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433369/SRX1433369.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433369/SRX1433369.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433369/SRX1433369.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433369/SRX1433369.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 18:00:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:00:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:00:33: 6000000 INFO @ Sun, 21 Jun 2020 18:00:35: 1000000 INFO @ Sun, 21 Jun 2020 18:00:40: 7000000 INFO @ Sun, 21 Jun 2020 18:00:42: 2000000 INFO @ Sun, 21 Jun 2020 18:00:47: 8000000 INFO @ Sun, 21 Jun 2020 18:00:48: 3000000 INFO @ Sun, 21 Jun 2020 18:00:53: 9000000 INFO @ Sun, 21 Jun 2020 18:00:55: 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 18:00:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433369/SRX1433369.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433369/SRX1433369.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433369/SRX1433369.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433369/SRX1433369.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 18:00:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:00:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:01:00: 10000000 INFO @ Sun, 21 Jun 2020 18:01:01: 5000000 INFO @ Sun, 21 Jun 2020 18:01:06: 1000000 INFO @ Sun, 21 Jun 2020 18:01:07: 11000000 INFO @ Sun, 21 Jun 2020 18:01:08: 6000000 INFO @ Sun, 21 Jun 2020 18:01:12: 2000000 INFO @ Sun, 21 Jun 2020 18:01:13: 12000000 INFO @ Sun, 21 Jun 2020 18:01:14: 7000000 INFO @ Sun, 21 Jun 2020 18:01:19: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:01:19: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:01:19: #1 total tags in treatment: 12796707 INFO @ Sun, 21 Jun 2020 18:01:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:01:19: #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 18:01:19: 3000000 INFO @ Sun, 21 Jun 2020 18:01:19: #1 tags after filtering in treatment: 12796618 INFO @ Sun, 21 Jun 2020 18:01:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:01:19: #1 finished! INFO @ Sun, 21 Jun 2020 18:01:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:01:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:01:20: #2 number of paired peaks: 609 WARNING @ Sun, 21 Jun 2020 18:01:20: Fewer paired peaks (609) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 609 pairs to build model! INFO @ Sun, 21 Jun 2020 18:01:20: start model_add_line... INFO @ Sun, 21 Jun 2020 18:01:20: start X-correlation... INFO @ Sun, 21 Jun 2020 18:01:20: end of X-cor INFO @ Sun, 21 Jun 2020 18:01:20: #2 finished! INFO @ Sun, 21 Jun 2020 18:01:20: #2 predicted fragment length is 125 bps INFO @ Sun, 21 Jun 2020 18:01:20: #2 alternative fragment length(s) may be 4,72,125 bps INFO @ Sun, 21 Jun 2020 18:01:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433369/SRX1433369.05_model.r INFO @ Sun, 21 Jun 2020 18:01:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:01:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:01:21: 8000000 INFO @ Sun, 21 Jun 2020 18:01:25: 4000000 INFO @ Sun, 21 Jun 2020 18:01:27: 9000000 INFO @ Sun, 21 Jun 2020 18:01:32: 5000000 INFO @ Sun, 21 Jun 2020 18:01:34: 10000000 INFO @ Sun, 21 Jun 2020 18:01:38: 6000000 INFO @ Sun, 21 Jun 2020 18:01:40: 11000000 INFO @ Sun, 21 Jun 2020 18:01:45: 7000000 INFO @ Sun, 21 Jun 2020 18:01:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:01:47: 12000000 INFO @ Sun, 21 Jun 2020 18:01:51: 8000000 INFO @ Sun, 21 Jun 2020 18:01:52: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:01:52: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:01:52: #1 total tags in treatment: 12796707 INFO @ Sun, 21 Jun 2020 18:01:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:01:52: #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 18:01:53: #1 tags after filtering in treatment: 12796618 INFO @ Sun, 21 Jun 2020 18:01:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:01:53: #1 finished! INFO @ Sun, 21 Jun 2020 18:01:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:01:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:01:53: #2 number of paired peaks: 609 WARNING @ Sun, 21 Jun 2020 18:01:53: Fewer paired peaks (609) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 609 pairs to build model! INFO @ Sun, 21 Jun 2020 18:01:53: start model_add_line... INFO @ Sun, 21 Jun 2020 18:01:54: start X-correlation... INFO @ Sun, 21 Jun 2020 18:01:54: end of X-cor INFO @ Sun, 21 Jun 2020 18:01:54: #2 finished! INFO @ Sun, 21 Jun 2020 18:01:54: #2 predicted fragment length is 125 bps INFO @ Sun, 21 Jun 2020 18:01:54: #2 alternative fragment length(s) may be 4,72,125 bps INFO @ Sun, 21 Jun 2020 18:01:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433369/SRX1433369.10_model.r INFO @ Sun, 21 Jun 2020 18:01:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:01:54: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:01:57: 9000000 INFO @ Sun, 21 Jun 2020 18:02:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433369/SRX1433369.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:02:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433369/SRX1433369.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:02:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433369/SRX1433369.05_summits.bed INFO @ Sun, 21 Jun 2020 18:02:00: Done! pass1 - making usageList (471 chroms): 1 millis pass2 - checking and writing primary data (1841 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:02:03: 10000000 INFO @ Sun, 21 Jun 2020 18:02:09: 11000000 INFO @ Sun, 21 Jun 2020 18:02:15: 12000000 INFO @ Sun, 21 Jun 2020 18:02:20: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:02:20: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:02:20: #1 total tags in treatment: 12796707 INFO @ Sun, 21 Jun 2020 18:02:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:02:20: #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 18:02:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:02:20: #1 tags after filtering in treatment: 12796618 INFO @ Sun, 21 Jun 2020 18:02:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:02:20: #1 finished! INFO @ Sun, 21 Jun 2020 18:02:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:02:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:02:21: #2 number of paired peaks: 609 WARNING @ Sun, 21 Jun 2020 18:02:21: Fewer paired peaks (609) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 609 pairs to build model! INFO @ Sun, 21 Jun 2020 18:02:21: start model_add_line... INFO @ Sun, 21 Jun 2020 18:02:21: start X-correlation... INFO @ Sun, 21 Jun 2020 18:02:21: end of X-cor INFO @ Sun, 21 Jun 2020 18:02:21: #2 finished! INFO @ Sun, 21 Jun 2020 18:02:21: #2 predicted fragment length is 125 bps INFO @ Sun, 21 Jun 2020 18:02:21: #2 alternative fragment length(s) may be 4,72,125 bps INFO @ Sun, 21 Jun 2020 18:02:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433369/SRX1433369.20_model.r INFO @ Sun, 21 Jun 2020 18:02:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:02:21: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:02:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433369/SRX1433369.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:02:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433369/SRX1433369.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:02:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433369/SRX1433369.10_summits.bed INFO @ Sun, 21 Jun 2020 18:02:32: Done! pass1 - making usageList (286 chroms): 1 millis pass2 - checking and writing primary data (781 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:02:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:03:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433369/SRX1433369.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:03:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433369/SRX1433369.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:03:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433369/SRX1433369.20_summits.bed INFO @ Sun, 21 Jun 2020 18:03:01: Done! pass1 - making usageList (109 chroms): 1 millis pass2 - checking and writing primary data (255 records, 4 fields): 5 millis CompletedMACS2peakCalling