Job ID = 6368490 SRX = SRX5020720 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:25:31 prefetch.2.10.7: 1) Downloading 'SRR8201343'... 2020-06-16T00:25:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:26:59 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:27:00 prefetch.2.10.7: 'SRR8201343' is valid 2020-06-16T00:27:00 prefetch.2.10.7: 1) 'SRR8201343' was downloaded successfully Read 9608336 spots for SRR8201343/SRR8201343.sra Written 9608336 spots for SRR8201343/SRR8201343.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: 00:02:08 9608336 reads; of these: 9608336 (100.00%) were unpaired; of these: 710747 (7.40%) aligned 0 times 7485891 (77.91%) aligned exactly 1 time 1411698 (14.69%) aligned >1 times 92.60% overall alignment rate Time searching: 00:02:08 Overall time: 00:02:08 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 686443 / 8897589 = 0.0771 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 @ Tue, 16 Jun 2020 09:32:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020720/SRX5020720.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020720/SRX5020720.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020720/SRX5020720.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020720/SRX5020720.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 09:32:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:32:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:32:40: 1000000 INFO @ Tue, 16 Jun 2020 09:32:46: 2000000 INFO @ Tue, 16 Jun 2020 09:32:53: 3000000 INFO @ Tue, 16 Jun 2020 09:32:59: 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 @ Tue, 16 Jun 2020 09:33:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020720/SRX5020720.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020720/SRX5020720.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020720/SRX5020720.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020720/SRX5020720.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 09:33:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:33:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:33:06: 5000000 INFO @ Tue, 16 Jun 2020 09:33:10: 1000000 INFO @ Tue, 16 Jun 2020 09:33:13: 6000000 INFO @ Tue, 16 Jun 2020 09:33:16: 2000000 INFO @ Tue, 16 Jun 2020 09:33:20: 7000000 INFO @ Tue, 16 Jun 2020 09:33:23: 3000000 INFO @ Tue, 16 Jun 2020 09:33:27: 8000000 INFO @ Tue, 16 Jun 2020 09:33:28: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:33:28: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:33:28: #1 total tags in treatment: 8211146 INFO @ Tue, 16 Jun 2020 09:33:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:33:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:33:28: #1 tags after filtering in treatment: 8211146 INFO @ Tue, 16 Jun 2020 09:33:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:33:28: #1 finished! INFO @ Tue, 16 Jun 2020 09:33:28: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:33:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:33:29: #2 number of paired peaks: 523 WARNING @ Tue, 16 Jun 2020 09:33:29: Fewer paired peaks (523) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 523 pairs to build model! INFO @ Tue, 16 Jun 2020 09:33:29: start model_add_line... INFO @ Tue, 16 Jun 2020 09:33:29: start X-correlation... INFO @ Tue, 16 Jun 2020 09:33:29: end of X-cor INFO @ Tue, 16 Jun 2020 09:33:29: #2 finished! INFO @ Tue, 16 Jun 2020 09:33:29: #2 predicted fragment length is 152 bps INFO @ Tue, 16 Jun 2020 09:33:29: #2 alternative fragment length(s) may be 152 bps INFO @ Tue, 16 Jun 2020 09:33:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020720/SRX5020720.05_model.r INFO @ Tue, 16 Jun 2020 09:33:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:33:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:33:30: 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 @ Tue, 16 Jun 2020 09:33:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020720/SRX5020720.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020720/SRX5020720.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020720/SRX5020720.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020720/SRX5020720.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 09:33:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:33:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:33:37: 5000000 INFO @ Tue, 16 Jun 2020 09:33:40: 1000000 INFO @ Tue, 16 Jun 2020 09:33:44: 6000000 INFO @ Tue, 16 Jun 2020 09:33:47: 2000000 INFO @ Tue, 16 Jun 2020 09:33:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:33:50: 7000000 INFO @ Tue, 16 Jun 2020 09:33:54: 3000000 INFO @ Tue, 16 Jun 2020 09:33:57: 8000000 INFO @ Tue, 16 Jun 2020 09:33:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020720/SRX5020720.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:33:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020720/SRX5020720.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:33:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020720/SRX5020720.05_summits.bed INFO @ Tue, 16 Jun 2020 09:33:58: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2891 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:33:59: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:33:59: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:33:59: #1 total tags in treatment: 8211146 INFO @ Tue, 16 Jun 2020 09:33:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:33:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:33:59: #1 tags after filtering in treatment: 8211146 INFO @ Tue, 16 Jun 2020 09:33:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:33:59: #1 finished! INFO @ Tue, 16 Jun 2020 09:33:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:33:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:33:59: #2 number of paired peaks: 523 WARNING @ Tue, 16 Jun 2020 09:33:59: Fewer paired peaks (523) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 523 pairs to build model! INFO @ Tue, 16 Jun 2020 09:33:59: start model_add_line... INFO @ Tue, 16 Jun 2020 09:33:59: start X-correlation... INFO @ Tue, 16 Jun 2020 09:33:59: end of X-cor INFO @ Tue, 16 Jun 2020 09:33:59: #2 finished! INFO @ Tue, 16 Jun 2020 09:33:59: #2 predicted fragment length is 152 bps INFO @ Tue, 16 Jun 2020 09:33:59: #2 alternative fragment length(s) may be 152 bps INFO @ Tue, 16 Jun 2020 09:33:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020720/SRX5020720.10_model.r INFO @ Tue, 16 Jun 2020 09:33:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:33:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:34:00: 4000000 INFO @ Tue, 16 Jun 2020 09:34:07: 5000000 INFO @ Tue, 16 Jun 2020 09:34:13: 6000000 INFO @ Tue, 16 Jun 2020 09:34:18: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:34:20: 7000000 INFO @ Tue, 16 Jun 2020 09:34:26: 8000000 INFO @ Tue, 16 Jun 2020 09:34:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020720/SRX5020720.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:34:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020720/SRX5020720.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:34:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020720/SRX5020720.10_summits.bed INFO @ Tue, 16 Jun 2020 09:34:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1242 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:34:28: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:34:28: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:34:28: #1 total tags in treatment: 8211146 INFO @ Tue, 16 Jun 2020 09:34:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:34:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:34:28: #1 tags after filtering in treatment: 8211146 INFO @ Tue, 16 Jun 2020 09:34:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:34:28: #1 finished! INFO @ Tue, 16 Jun 2020 09:34:28: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:34:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:34:29: #2 number of paired peaks: 523 WARNING @ Tue, 16 Jun 2020 09:34:29: Fewer paired peaks (523) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 523 pairs to build model! INFO @ Tue, 16 Jun 2020 09:34:29: start model_add_line... INFO @ Tue, 16 Jun 2020 09:34:29: start X-correlation... INFO @ Tue, 16 Jun 2020 09:34:29: end of X-cor INFO @ Tue, 16 Jun 2020 09:34:29: #2 finished! INFO @ Tue, 16 Jun 2020 09:34:29: #2 predicted fragment length is 152 bps INFO @ Tue, 16 Jun 2020 09:34:29: #2 alternative fragment length(s) may be 152 bps INFO @ Tue, 16 Jun 2020 09:34:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020720/SRX5020720.20_model.r INFO @ Tue, 16 Jun 2020 09:34:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:34:29: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:34:47: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:34:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020720/SRX5020720.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:34:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020720/SRX5020720.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:34:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020720/SRX5020720.20_summits.bed INFO @ Tue, 16 Jun 2020 09:34:57: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (391 records, 4 fields): 2 millis CompletedMACS2peakCalling