Job ID = 6369048 SRX = SRX997747 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:41:43 prefetch.2.10.7: 1) Downloading 'SRR1977494'... 2020-06-16T00:41:43 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:47:30 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:47:30 prefetch.2.10.7: 1) 'SRR1977494' was downloaded successfully Read 37754539 spots for SRR1977494/SRR1977494.sra Written 37754539 spots for SRR1977494/SRR1977494.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: 00:04:58 37754539 reads; of these: 37754539 (100.00%) were unpaired; of these: 17760232 (47.04%) aligned 0 times 16188395 (42.88%) aligned exactly 1 time 3805912 (10.08%) aligned >1 times 52.96% overall alignment rate Time searching: 00:04:58 Overall time: 00:04:59 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] 12553394 / 19994307 = 0.6278 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 09:57:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX997747/SRX997747.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX997747/SRX997747.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX997747/SRX997747.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX997747/SRX997747.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 09:57:51: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:57:51: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:57:55: 1000000 INFO @ Tue, 16 Jun 2020 09:58:00: 2000000 INFO @ Tue, 16 Jun 2020 09:58:05: 3000000 INFO @ Tue, 16 Jun 2020 09:58:09: 4000000 INFO @ Tue, 16 Jun 2020 09:58:14: 5000000 INFO @ Tue, 16 Jun 2020 09:58:18: 6000000 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 09:58:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX997747/SRX997747.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX997747/SRX997747.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX997747/SRX997747.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX997747/SRX997747.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 09:58:21: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:58:21: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:58:23: 7000000 INFO @ Tue, 16 Jun 2020 09:58:25: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:58:25: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:58:25: #1 total tags in treatment: 7440913 INFO @ Tue, 16 Jun 2020 09:58:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:58:25: #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 09:58:25: #1 tags after filtering in treatment: 7440913 INFO @ Tue, 16 Jun 2020 09:58:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:58:25: #1 finished! INFO @ Tue, 16 Jun 2020 09:58:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:58:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:58:25: #2 number of paired peaks: 1207 INFO @ Tue, 16 Jun 2020 09:58:25: start model_add_line... INFO @ Tue, 16 Jun 2020 09:58:26: start X-correlation... INFO @ Tue, 16 Jun 2020 09:58:26: end of X-cor INFO @ Tue, 16 Jun 2020 09:58:26: #2 finished! INFO @ Tue, 16 Jun 2020 09:58:26: #2 predicted fragment length is 156 bps INFO @ Tue, 16 Jun 2020 09:58:26: #2 alternative fragment length(s) may be 156 bps INFO @ Tue, 16 Jun 2020 09:58:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX997747/SRX997747.05_model.r INFO @ Tue, 16 Jun 2020 09:58:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:58:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:58:26: 1000000 INFO @ Tue, 16 Jun 2020 09:58:31: 2000000 INFO @ Tue, 16 Jun 2020 09:58:36: 3000000 INFO @ Tue, 16 Jun 2020 09:58:41: 4000000 INFO @ Tue, 16 Jun 2020 09:58:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:58:46: 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 09:58:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX997747/SRX997747.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX997747/SRX997747.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX997747/SRX997747.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX997747/SRX997747.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 09:58:51: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:58:51: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:58:51: 6000000 INFO @ Tue, 16 Jun 2020 09:58:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX997747/SRX997747.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:58:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX997747/SRX997747.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:58:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX997747/SRX997747.05_summits.bed INFO @ Tue, 16 Jun 2020 09:58:54: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (8524 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:58:56: 1000000 INFO @ Tue, 16 Jun 2020 09:58:56: 7000000 INFO @ Tue, 16 Jun 2020 09:58:59: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:58:59: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:58:59: #1 total tags in treatment: 7440913 INFO @ Tue, 16 Jun 2020 09:58:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:58:59: #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 09:58:59: #1 tags after filtering in treatment: 7440913 INFO @ Tue, 16 Jun 2020 09:58:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:58:59: #1 finished! INFO @ Tue, 16 Jun 2020 09:58:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:58:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:58:59: #2 number of paired peaks: 1207 INFO @ Tue, 16 Jun 2020 09:58:59: start model_add_line... INFO @ Tue, 16 Jun 2020 09:58:59: start X-correlation... INFO @ Tue, 16 Jun 2020 09:58:59: end of X-cor INFO @ Tue, 16 Jun 2020 09:58:59: #2 finished! INFO @ Tue, 16 Jun 2020 09:58:59: #2 predicted fragment length is 156 bps INFO @ Tue, 16 Jun 2020 09:58:59: #2 alternative fragment length(s) may be 156 bps INFO @ Tue, 16 Jun 2020 09:58:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX997747/SRX997747.10_model.r INFO @ Tue, 16 Jun 2020 09:58:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:58:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:59:00: 2000000 INFO @ Tue, 16 Jun 2020 09:59:05: 3000000 INFO @ Tue, 16 Jun 2020 09:59:09: 4000000 INFO @ Tue, 16 Jun 2020 09:59:14: 5000000 INFO @ Tue, 16 Jun 2020 09:59:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:59:19: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:59:23: 7000000 INFO @ Tue, 16 Jun 2020 09:59:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX997747/SRX997747.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:59:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX997747/SRX997747.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:59:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX997747/SRX997747.10_summits.bed INFO @ Tue, 16 Jun 2020 09:59:25: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5288 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:59:25: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:59:25: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:59:25: #1 total tags in treatment: 7440913 INFO @ Tue, 16 Jun 2020 09:59:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:59:25: #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 09:59:25: #1 tags after filtering in treatment: 7440913 INFO @ Tue, 16 Jun 2020 09:59:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:59:25: #1 finished! INFO @ Tue, 16 Jun 2020 09:59:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:59:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:59:26: #2 number of paired peaks: 1207 INFO @ Tue, 16 Jun 2020 09:59:26: start model_add_line... INFO @ Tue, 16 Jun 2020 09:59:26: start X-correlation... INFO @ Tue, 16 Jun 2020 09:59:26: end of X-cor INFO @ Tue, 16 Jun 2020 09:59:26: #2 finished! INFO @ Tue, 16 Jun 2020 09:59:26: #2 predicted fragment length is 156 bps INFO @ Tue, 16 Jun 2020 09:59:26: #2 alternative fragment length(s) may be 156 bps INFO @ Tue, 16 Jun 2020 09:59:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX997747/SRX997747.20_model.r INFO @ Tue, 16 Jun 2020 09:59:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:59:26: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:59:45: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:59:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX997747/SRX997747.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:59:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX997747/SRX997747.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:59:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX997747/SRX997747.20_summits.bed INFO @ Tue, 16 Jun 2020 09:59:54: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2952 records, 4 fields): 4 millis CompletedMACS2peakCalling