Job ID = 6497472 SRX = SRX494973 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T21:57:39 prefetch.2.10.7: 1) Downloading 'SRR1198505'... 2020-06-25T21:57:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T21:59:45 prefetch.2.10.7: HTTPS download succeed 2020-06-25T21:59:46 prefetch.2.10.7: 'SRR1198505' is valid 2020-06-25T21:59:46 prefetch.2.10.7: 1) 'SRR1198505' was downloaded successfully Read 14762597 spots for SRR1198505/SRR1198505.sra Written 14762597 spots for SRR1198505/SRR1198505.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:15 14762597 reads; of these: 14762597 (100.00%) were unpaired; of these: 932235 (6.31%) aligned 0 times 11693013 (79.21%) aligned exactly 1 time 2137349 (14.48%) aligned >1 times 93.69% overall alignment rate Time searching: 00:03:16 Overall time: 00:03:16 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] 9682250 / 13830362 = 0.7001 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 @ Fri, 26 Jun 2020 07:07:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494973/SRX494973.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494973/SRX494973.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494973/SRX494973.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494973/SRX494973.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 @ Fri, 26 Jun 2020 07:07:27: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:07:27: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:07:33: 1000000 INFO @ Fri, 26 Jun 2020 07:07:39: 2000000 INFO @ Fri, 26 Jun 2020 07:07:45: 3000000 INFO @ Fri, 26 Jun 2020 07:07:51: 4000000 INFO @ Fri, 26 Jun 2020 07:07:51: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:07:51: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:07:51: #1 total tags in treatment: 4148112 INFO @ Fri, 26 Jun 2020 07:07:51: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:07:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:07:51: #1 tags after filtering in treatment: 4148112 INFO @ Fri, 26 Jun 2020 07:07:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:07:51: #1 finished! INFO @ Fri, 26 Jun 2020 07:07:51: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:07:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:07:52: #2 number of paired peaks: 2520 INFO @ Fri, 26 Jun 2020 07:07:52: start model_add_line... INFO @ Fri, 26 Jun 2020 07:07:52: start X-correlation... INFO @ Fri, 26 Jun 2020 07:07:52: end of X-cor INFO @ Fri, 26 Jun 2020 07:07:52: #2 finished! INFO @ Fri, 26 Jun 2020 07:07:52: #2 predicted fragment length is 112 bps INFO @ Fri, 26 Jun 2020 07:07:52: #2 alternative fragment length(s) may be 112 bps INFO @ Fri, 26 Jun 2020 07:07:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494973/SRX494973.05_model.r INFO @ Fri, 26 Jun 2020 07:07:52: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:07:52: #3 Pre-compute pvalue-qvalue table... 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 @ Fri, 26 Jun 2020 07:07:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494973/SRX494973.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494973/SRX494973.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494973/SRX494973.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494973/SRX494973.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 @ Fri, 26 Jun 2020 07:07:57: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:07:57: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:08:02: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:08:03: 1000000 INFO @ Fri, 26 Jun 2020 07:08:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494973/SRX494973.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:08:09: 2000000 INFO @ Fri, 26 Jun 2020 07:08:15: 3000000 INFO @ Fri, 26 Jun 2020 07:08:21: 4000000 INFO @ Fri, 26 Jun 2020 07:08:22: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:08:22: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:08:22: #1 total tags in treatment: 4148112 INFO @ Fri, 26 Jun 2020 07:08:22: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:08:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:08:22: #1 tags after filtering in treatment: 4148112 INFO @ Fri, 26 Jun 2020 07:08:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:08:22: #1 finished! INFO @ Fri, 26 Jun 2020 07:08:22: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:08:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:08:22: #2 number of paired peaks: 2520 INFO @ Fri, 26 Jun 2020 07:08:22: start model_add_line... INFO @ Fri, 26 Jun 2020 07:08:22: start X-correlation... INFO @ Fri, 26 Jun 2020 07:08:22: end of X-cor INFO @ Fri, 26 Jun 2020 07:08:22: #2 finished! INFO @ Fri, 26 Jun 2020 07:08:22: #2 predicted fragment length is 112 bps INFO @ Fri, 26 Jun 2020 07:08:22: #2 alternative fragment length(s) may be 112 bps INFO @ Fri, 26 Jun 2020 07:08:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494973/SRX494973.10_model.r BedGraph に変換中... INFO @ Fri, 26 Jun 2020 07:08:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494973/SRX494973.05_peaks.narrowPeak 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 @ Fri, 26 Jun 2020 07:09:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494973/SRX494973.05_summits.bed INFO @ Fri, 26 Jun 2020 07:09:00: Done! INFO @ Fri, 26 Jun 2020 07:09:00: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:09:00: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4163 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:09:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494973/SRX494973.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494973/SRX494973.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494973/SRX494973.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494973/SRX494973.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 @ Fri, 26 Jun 2020 07:09:02: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:09:02: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:09:09: 1000000 INFO @ Fri, 26 Jun 2020 07:09:10: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:09:15: 2000000 INFO @ Fri, 26 Jun 2020 07:09:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494973/SRX494973.10_peaks.xls BedGraph に変換しました。 INFO @ Fri, 26 Jun 2020 07:09:21: 3000000 INFO @ Fri, 26 Jun 2020 07:09:27: 4000000 INFO @ Fri, 26 Jun 2020 07:09:28: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:09:28: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:09:28: #1 total tags in treatment: 4148112 INFO @ Fri, 26 Jun 2020 07:09:28: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:09:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:09:28: #1 tags after filtering in treatment: 4148112 INFO @ Fri, 26 Jun 2020 07:09:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:09:28: #1 finished! INFO @ Fri, 26 Jun 2020 07:09:28: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:09:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:09:29: #2 number of paired peaks: 2520 INFO @ Fri, 26 Jun 2020 07:09:29: start model_add_line... INFO @ Fri, 26 Jun 2020 07:09:29: start X-correlation... INFO @ Fri, 26 Jun 2020 07:09:29: end of X-cor INFO @ Fri, 26 Jun 2020 07:09:29: #2 finished! INFO @ Fri, 26 Jun 2020 07:09:29: #2 predicted fragment length is 112 bps INFO @ Fri, 26 Jun 2020 07:09:29: #2 alternative fragment length(s) may be 112 bps INFO @ Fri, 26 Jun 2020 07:09:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494973/SRX494973.20_model.r INFO @ Fri, 26 Jun 2020 07:09:35: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:09:35: #3 Pre-compute pvalue-qvalue table... BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:09:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494973/SRX494973.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:09:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494973/SRX494973.10_summits.bed INFO @ Fri, 26 Jun 2020 07:09:35: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3148 records, 4 fields): 6 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:09:46: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:09:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494973/SRX494973.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:09:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494973/SRX494973.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:09:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494973/SRX494973.20_summits.bed INFO @ Fri, 26 Jun 2020 07:09:55: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2183 records, 4 fields): 3 millis CompletedMACS2peakCalling