Job ID = 6367135 SRX = SRX277093 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:24:05 prefetch.2.10.7: 1) Downloading 'SRR849769'... 2020-06-15T23:24:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:24:29 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:24:29 prefetch.2.10.7: 'SRR849769' is valid 2020-06-15T23:24:29 prefetch.2.10.7: 1) 'SRR849769' was downloaded successfully Read 6859700 spots for SRR849769/SRR849769.sra Written 6859700 spots for SRR849769/SRR849769.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: 00:01:05 6859700 reads; of these: 6859700 (100.00%) were unpaired; of these: 741548 (10.81%) aligned 0 times 5253452 (76.58%) aligned exactly 1 time 864700 (12.61%) aligned >1 times 89.19% overall alignment rate Time searching: 00:01:05 Overall time: 00:01:05 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] 999987 / 6118152 = 0.1634 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 08:27:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277093/SRX277093.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277093/SRX277093.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277093/SRX277093.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277093/SRX277093.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 08:27:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:27:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:27:41: 1000000 INFO @ Tue, 16 Jun 2020 08:27:46: 2000000 INFO @ Tue, 16 Jun 2020 08:27:52: 3000000 INFO @ Tue, 16 Jun 2020 08:27:57: 4000000 INFO @ Tue, 16 Jun 2020 08:28:03: 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 08:28:03: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:28:03: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:28:03: #1 total tags in treatment: 5118165 INFO @ Tue, 16 Jun 2020 08:28:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:28:03: #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 08:28:03: #1 tags after filtering in treatment: 5118165 INFO @ Tue, 16 Jun 2020 08:28:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:28:03: #1 finished! INFO @ Tue, 16 Jun 2020 08:28:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:28:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:28:04: #2 number of paired peaks: 862 WARNING @ Tue, 16 Jun 2020 08:28:04: Fewer paired peaks (862) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 862 pairs to build model! INFO @ Tue, 16 Jun 2020 08:28:04: start model_add_line... INFO @ Tue, 16 Jun 2020 08:28:04: start X-correlation... INFO @ Tue, 16 Jun 2020 08:28:04: end of X-cor INFO @ Tue, 16 Jun 2020 08:28:04: #2 finished! INFO @ Tue, 16 Jun 2020 08:28:04: #2 predicted fragment length is 132 bps INFO @ Tue, 16 Jun 2020 08:28:04: #2 alternative fragment length(s) may be 132 bps INFO @ Tue, 16 Jun 2020 08:28:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277093/SRX277093.05_model.r INFO @ Tue, 16 Jun 2020 08:28:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:28:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:28:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277093/SRX277093.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277093/SRX277093.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277093/SRX277093.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277093/SRX277093.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 08:28:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:28:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:28:11: 1000000 INFO @ Tue, 16 Jun 2020 08:28:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:28:18: 2000000 INFO @ Tue, 16 Jun 2020 08:28:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277093/SRX277093.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:28:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277093/SRX277093.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:28:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277093/SRX277093.05_summits.bed INFO @ Tue, 16 Jun 2020 08:28:23: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (3458 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:28:24: 3000000 INFO @ Tue, 16 Jun 2020 08:28:30: 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 08:28:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277093/SRX277093.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277093/SRX277093.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277093/SRX277093.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277093/SRX277093.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 08:28:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:28:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:28:35: 5000000 INFO @ Tue, 16 Jun 2020 08:28:36: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:28:36: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:28:36: #1 total tags in treatment: 5118165 INFO @ Tue, 16 Jun 2020 08:28:36: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:28:36: #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 08:28:36: #1 tags after filtering in treatment: 5118165 INFO @ Tue, 16 Jun 2020 08:28:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:28:36: #1 finished! INFO @ Tue, 16 Jun 2020 08:28:36: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:28:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:28:36: #2 number of paired peaks: 862 WARNING @ Tue, 16 Jun 2020 08:28:36: Fewer paired peaks (862) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 862 pairs to build model! INFO @ Tue, 16 Jun 2020 08:28:36: start model_add_line... INFO @ Tue, 16 Jun 2020 08:28:36: start X-correlation... INFO @ Tue, 16 Jun 2020 08:28:36: end of X-cor INFO @ Tue, 16 Jun 2020 08:28:36: #2 finished! INFO @ Tue, 16 Jun 2020 08:28:36: #2 predicted fragment length is 132 bps INFO @ Tue, 16 Jun 2020 08:28:36: #2 alternative fragment length(s) may be 132 bps INFO @ Tue, 16 Jun 2020 08:28:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277093/SRX277093.10_model.r INFO @ Tue, 16 Jun 2020 08:28:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:28:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:28:40: 1000000 INFO @ Tue, 16 Jun 2020 08:28:46: 2000000 INFO @ Tue, 16 Jun 2020 08:28:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:28:51: 3000000 INFO @ Tue, 16 Jun 2020 08:28:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277093/SRX277093.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:28:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277093/SRX277093.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:28:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277093/SRX277093.10_summits.bed INFO @ Tue, 16 Jun 2020 08:28:54: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (2017 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:28:56: 4000000 INFO @ Tue, 16 Jun 2020 08:29:01: 5000000 INFO @ Tue, 16 Jun 2020 08:29:02: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:29:02: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:29:02: #1 total tags in treatment: 5118165 INFO @ Tue, 16 Jun 2020 08:29:02: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:29:02: #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 08:29:02: #1 tags after filtering in treatment: 5118165 INFO @ Tue, 16 Jun 2020 08:29:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:29:02: #1 finished! INFO @ Tue, 16 Jun 2020 08:29:02: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:29:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:29:02: #2 number of paired peaks: 862 WARNING @ Tue, 16 Jun 2020 08:29:02: Fewer paired peaks (862) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 862 pairs to build model! INFO @ Tue, 16 Jun 2020 08:29:02: start model_add_line... INFO @ Tue, 16 Jun 2020 08:29:02: start X-correlation... INFO @ Tue, 16 Jun 2020 08:29:02: end of X-cor INFO @ Tue, 16 Jun 2020 08:29:02: #2 finished! INFO @ Tue, 16 Jun 2020 08:29:02: #2 predicted fragment length is 132 bps INFO @ Tue, 16 Jun 2020 08:29:02: #2 alternative fragment length(s) may be 132 bps INFO @ Tue, 16 Jun 2020 08:29:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277093/SRX277093.20_model.r INFO @ Tue, 16 Jun 2020 08:29:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:29:02: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:29:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:29:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277093/SRX277093.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:29:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277093/SRX277093.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:29:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277093/SRX277093.20_summits.bed INFO @ Tue, 16 Jun 2020 08:29:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (854 records, 4 fields): 2 millis CompletedMACS2peakCalling