Job ID = 6368273 SRX = SRX494957 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:52:18 prefetch.2.10.7: 1) Downloading 'SRR1198489'... 2020-06-15T23:52:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:54:20 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:54:21 prefetch.2.10.7: 'SRR1198489' is valid 2020-06-15T23:54:21 prefetch.2.10.7: 1) 'SRR1198489' was downloaded successfully Read 17778538 spots for SRR1198489/SRR1198489.sra Written 17778538 spots for SRR1198489/SRR1198489.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: 00:02:46 17778538 reads; of these: 17778538 (100.00%) were unpaired; of these: 747606 (4.21%) aligned 0 times 13796462 (77.60%) aligned exactly 1 time 3234470 (18.19%) aligned >1 times 95.79% overall alignment rate Time searching: 00:02:46 Overall time: 00:02:46 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_sort_core] merging from 8 files... [bam_rmdupse_core] 2484729 / 17030932 = 0.1459 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 09:02:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494957/SRX494957.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494957/SRX494957.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494957/SRX494957.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494957/SRX494957.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 09:02:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:02:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:02:43: 1000000 INFO @ Tue, 16 Jun 2020 09:02:48: 2000000 INFO @ Tue, 16 Jun 2020 09:02:53: 3000000 INFO @ Tue, 16 Jun 2020 09:02:58: 4000000 INFO @ Tue, 16 Jun 2020 09:03:03: 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 @ Tue, 16 Jun 2020 09:03:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494957/SRX494957.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494957/SRX494957.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494957/SRX494957.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494957/SRX494957.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 09:03:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:03:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:03:08: 6000000 INFO @ Tue, 16 Jun 2020 09:03:14: 1000000 INFO @ Tue, 16 Jun 2020 09:03:14: 7000000 INFO @ Tue, 16 Jun 2020 09:03:19: 2000000 INFO @ Tue, 16 Jun 2020 09:03:19: 8000000 INFO @ Tue, 16 Jun 2020 09:03:25: 3000000 INFO @ Tue, 16 Jun 2020 09:03:25: 9000000 INFO @ Tue, 16 Jun 2020 09:03:30: 4000000 INFO @ Tue, 16 Jun 2020 09:03:30: 10000000 INFO @ Tue, 16 Jun 2020 09:03:35: 11000000 INFO @ Tue, 16 Jun 2020 09:03:35: 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 @ Tue, 16 Jun 2020 09:03:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494957/SRX494957.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494957/SRX494957.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494957/SRX494957.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494957/SRX494957.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 09:03:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:03:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:03:41: 12000000 INFO @ Tue, 16 Jun 2020 09:03:41: 6000000 INFO @ Tue, 16 Jun 2020 09:03:44: 1000000 INFO @ Tue, 16 Jun 2020 09:03:46: 13000000 INFO @ Tue, 16 Jun 2020 09:03:47: 7000000 INFO @ Tue, 16 Jun 2020 09:03:49: 2000000 INFO @ Tue, 16 Jun 2020 09:03:52: 14000000 INFO @ Tue, 16 Jun 2020 09:03:52: 8000000 INFO @ Tue, 16 Jun 2020 09:03:55: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:03:55: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:03:55: #1 total tags in treatment: 14546203 INFO @ Tue, 16 Jun 2020 09:03:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:03:55: #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 09:03:55: 3000000 INFO @ Tue, 16 Jun 2020 09:03:55: #1 tags after filtering in treatment: 14546203 INFO @ Tue, 16 Jun 2020 09:03:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:03:55: #1 finished! INFO @ Tue, 16 Jun 2020 09:03:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:03:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:03:56: #2 number of paired peaks: 426 WARNING @ Tue, 16 Jun 2020 09:03:56: Fewer paired peaks (426) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 426 pairs to build model! INFO @ Tue, 16 Jun 2020 09:03:56: start model_add_line... INFO @ Tue, 16 Jun 2020 09:03:56: start X-correlation... INFO @ Tue, 16 Jun 2020 09:03:56: end of X-cor INFO @ Tue, 16 Jun 2020 09:03:56: #2 finished! INFO @ Tue, 16 Jun 2020 09:03:56: #2 predicted fragment length is 75 bps INFO @ Tue, 16 Jun 2020 09:03:56: #2 alternative fragment length(s) may be 3,75 bps INFO @ Tue, 16 Jun 2020 09:03:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494957/SRX494957.05_model.r INFO @ Tue, 16 Jun 2020 09:03:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:03:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:03:58: 9000000 INFO @ Tue, 16 Jun 2020 09:04:00: 4000000 INFO @ Tue, 16 Jun 2020 09:04:03: 10000000 INFO @ Tue, 16 Jun 2020 09:04:06: 5000000 INFO @ Tue, 16 Jun 2020 09:04:08: 11000000 INFO @ Tue, 16 Jun 2020 09:04:11: 6000000 INFO @ Tue, 16 Jun 2020 09:04:14: 12000000 INFO @ Tue, 16 Jun 2020 09:04:16: 7000000 INFO @ Tue, 16 Jun 2020 09:04:19: 13000000 INFO @ Tue, 16 Jun 2020 09:04:22: 8000000 INFO @ Tue, 16 Jun 2020 09:04:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:04:24: 14000000 INFO @ Tue, 16 Jun 2020 09:04:27: 9000000 INFO @ Tue, 16 Jun 2020 09:04:27: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:04:27: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:04:27: #1 total tags in treatment: 14546203 INFO @ Tue, 16 Jun 2020 09:04:27: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:04:27: #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 09:04:27: #1 tags after filtering in treatment: 14546203 INFO @ Tue, 16 Jun 2020 09:04:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:04:27: #1 finished! INFO @ Tue, 16 Jun 2020 09:04:27: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:04:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:04:28: #2 number of paired peaks: 426 WARNING @ Tue, 16 Jun 2020 09:04:28: Fewer paired peaks (426) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 426 pairs to build model! INFO @ Tue, 16 Jun 2020 09:04:28: start model_add_line... INFO @ Tue, 16 Jun 2020 09:04:29: start X-correlation... INFO @ Tue, 16 Jun 2020 09:04:29: end of X-cor INFO @ Tue, 16 Jun 2020 09:04:29: #2 finished! INFO @ Tue, 16 Jun 2020 09:04:29: #2 predicted fragment length is 75 bps INFO @ Tue, 16 Jun 2020 09:04:29: #2 alternative fragment length(s) may be 3,75 bps INFO @ Tue, 16 Jun 2020 09:04:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494957/SRX494957.10_model.r INFO @ Tue, 16 Jun 2020 09:04:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:04:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:04:32: 10000000 INFO @ Tue, 16 Jun 2020 09:04:37: 11000000 INFO @ Tue, 16 Jun 2020 09:04:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494957/SRX494957.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:04:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494957/SRX494957.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:04:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494957/SRX494957.05_summits.bed INFO @ Tue, 16 Jun 2020 09:04:38: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (9182 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:04:42: 12000000 INFO @ Tue, 16 Jun 2020 09:04:47: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:04:52: 14000000 INFO @ Tue, 16 Jun 2020 09:04:55: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:04:55: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:04:55: #1 total tags in treatment: 14546203 INFO @ Tue, 16 Jun 2020 09:04:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:04:55: #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 09:04:55: #1 tags after filtering in treatment: 14546203 INFO @ Tue, 16 Jun 2020 09:04:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:04:55: #1 finished! INFO @ Tue, 16 Jun 2020 09:04:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:04:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:04:55: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:04:56: #2 number of paired peaks: 426 WARNING @ Tue, 16 Jun 2020 09:04:56: Fewer paired peaks (426) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 426 pairs to build model! INFO @ Tue, 16 Jun 2020 09:04:56: start model_add_line... INFO @ Tue, 16 Jun 2020 09:04:56: start X-correlation... INFO @ Tue, 16 Jun 2020 09:04:56: end of X-cor INFO @ Tue, 16 Jun 2020 09:04:56: #2 finished! INFO @ Tue, 16 Jun 2020 09:04:56: #2 predicted fragment length is 75 bps INFO @ Tue, 16 Jun 2020 09:04:56: #2 alternative fragment length(s) may be 3,75 bps INFO @ Tue, 16 Jun 2020 09:04:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494957/SRX494957.20_model.r INFO @ Tue, 16 Jun 2020 09:04:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:04:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:05:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494957/SRX494957.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:05:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494957/SRX494957.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:05:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494957/SRX494957.10_summits.bed INFO @ Tue, 16 Jun 2020 09:05:08: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4733 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:05:21: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:05:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494957/SRX494957.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:05:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494957/SRX494957.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:05:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494957/SRX494957.20_summits.bed INFO @ Tue, 16 Jun 2020 09:05:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1721 records, 4 fields): 3 millis CompletedMACS2peakCalling