Job ID = 6367329 SRX = SRX331091 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:39:29 prefetch.2.10.7: 1) Downloading 'SRR947321'... 2020-06-15T23:39:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:40:17 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:40:17 prefetch.2.10.7: 'SRR947321' is valid 2020-06-15T23:40:17 prefetch.2.10.7: 1) 'SRR947321' was downloaded successfully Read 5182222 spots for SRR947321/SRR947321.sra Written 5182222 spots for SRR947321/SRR947321.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: 00:00:45 5182222 reads; of these: 5182222 (100.00%) were unpaired; of these: 102051 (1.97%) aligned 0 times 4325590 (83.47%) aligned exactly 1 time 754581 (14.56%) aligned >1 times 98.03% overall alignment rate Time searching: 00:00:45 Overall time: 00:00:45 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] 442122 / 5080171 = 0.0870 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 08:42:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331091/SRX331091.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331091/SRX331091.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331091/SRX331091.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331091/SRX331091.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 08:42:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:42:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:42:44: 1000000 INFO @ Tue, 16 Jun 2020 08:42:49: 2000000 INFO @ Tue, 16 Jun 2020 08:42:53: 3000000 INFO @ Tue, 16 Jun 2020 08:42:58: 4000000 INFO @ Tue, 16 Jun 2020 08:43:01: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:43:01: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:43:01: #1 total tags in treatment: 4638049 INFO @ Tue, 16 Jun 2020 08:43:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:43:01: #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 08:43:01: #1 tags after filtering in treatment: 4638049 INFO @ Tue, 16 Jun 2020 08:43:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:43:01: #1 finished! INFO @ Tue, 16 Jun 2020 08:43:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:43:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:43:01: #2 number of paired peaks: 329 WARNING @ Tue, 16 Jun 2020 08:43:01: Fewer paired peaks (329) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 329 pairs to build model! INFO @ Tue, 16 Jun 2020 08:43:01: start model_add_line... INFO @ Tue, 16 Jun 2020 08:43:01: start X-correlation... INFO @ Tue, 16 Jun 2020 08:43:01: end of X-cor INFO @ Tue, 16 Jun 2020 08:43:01: #2 finished! INFO @ Tue, 16 Jun 2020 08:43:01: #2 predicted fragment length is 75 bps INFO @ Tue, 16 Jun 2020 08:43:01: #2 alternative fragment length(s) may be 2,48,75,527,558,575,592 bps INFO @ Tue, 16 Jun 2020 08:43:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331091/SRX331091.05_model.r INFO @ Tue, 16 Jun 2020 08:43:01: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:43:01: #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 @ Tue, 16 Jun 2020 08:43:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331091/SRX331091.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331091/SRX331091.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331091/SRX331091.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331091/SRX331091.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 08:43:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:43:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:43:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:43:14: 1000000 INFO @ Tue, 16 Jun 2020 08:43:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331091/SRX331091.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:43:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331091/SRX331091.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:43:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331091/SRX331091.05_summits.bed INFO @ Tue, 16 Jun 2020 08:43:16: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (319 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:43:19: 2000000 INFO @ Tue, 16 Jun 2020 08:43:24: 3000000 INFO @ Tue, 16 Jun 2020 08:43:29: 4000000 INFO @ Tue, 16 Jun 2020 08:43:32: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:43:32: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:43:32: #1 total tags in treatment: 4638049 INFO @ Tue, 16 Jun 2020 08:43:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:43:32: #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 08:43:32: #1 tags after filtering in treatment: 4638049 INFO @ Tue, 16 Jun 2020 08:43:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:43:32: #1 finished! INFO @ Tue, 16 Jun 2020 08:43:32: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:43:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:43:32: #2 number of paired peaks: 329 WARNING @ Tue, 16 Jun 2020 08:43:32: Fewer paired peaks (329) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 329 pairs to build model! INFO @ Tue, 16 Jun 2020 08:43:32: start model_add_line... INFO @ Tue, 16 Jun 2020 08:43:32: start X-correlation... INFO @ Tue, 16 Jun 2020 08:43:32: end of X-cor INFO @ Tue, 16 Jun 2020 08:43:32: #2 finished! INFO @ Tue, 16 Jun 2020 08:43:32: #2 predicted fragment length is 75 bps INFO @ Tue, 16 Jun 2020 08:43:32: #2 alternative fragment length(s) may be 2,48,75,527,558,575,592 bps INFO @ Tue, 16 Jun 2020 08:43:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331091/SRX331091.10_model.r INFO @ Tue, 16 Jun 2020 08:43:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:43:32: #3 Pre-compute pvalue-qvalue table... 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 08:43:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331091/SRX331091.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331091/SRX331091.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331091/SRX331091.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331091/SRX331091.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 08:43:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:43:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:43:42: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:43:44: 1000000 INFO @ Tue, 16 Jun 2020 08:43:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331091/SRX331091.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:43:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331091/SRX331091.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:43:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331091/SRX331091.10_summits.bed INFO @ Tue, 16 Jun 2020 08:43:47: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (139 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:43:49: 2000000 INFO @ Tue, 16 Jun 2020 08:43:55: 3000000 INFO @ Tue, 16 Jun 2020 08:44:00: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:44:03: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:44:03: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:44:03: #1 total tags in treatment: 4638049 INFO @ Tue, 16 Jun 2020 08:44:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:44:03: #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 08:44:03: #1 tags after filtering in treatment: 4638049 INFO @ Tue, 16 Jun 2020 08:44:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:44:03: #1 finished! INFO @ Tue, 16 Jun 2020 08:44:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:44:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:44:04: #2 number of paired peaks: 329 WARNING @ Tue, 16 Jun 2020 08:44:04: Fewer paired peaks (329) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 329 pairs to build model! INFO @ Tue, 16 Jun 2020 08:44:04: start model_add_line... INFO @ Tue, 16 Jun 2020 08:44:04: start X-correlation... INFO @ Tue, 16 Jun 2020 08:44:04: end of X-cor INFO @ Tue, 16 Jun 2020 08:44:04: #2 finished! INFO @ Tue, 16 Jun 2020 08:44:04: #2 predicted fragment length is 75 bps INFO @ Tue, 16 Jun 2020 08:44:04: #2 alternative fragment length(s) may be 2,48,75,527,558,575,592 bps INFO @ Tue, 16 Jun 2020 08:44:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331091/SRX331091.20_model.r INFO @ Tue, 16 Jun 2020 08:44:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:44:04: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:44:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:44:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331091/SRX331091.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:44:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331091/SRX331091.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:44:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331091/SRX331091.20_summits.bed INFO @ Tue, 16 Jun 2020 08:44:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (58 records, 4 fields): 2 millis CompletedMACS2peakCalling