Job ID = 6367112 SRX = SRX277069 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:20:46 prefetch.2.10.7: 1) Downloading 'SRR849745'... 2020-06-15T23:20:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:21:12 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:21:12 prefetch.2.10.7: 'SRR849745' is valid 2020-06-15T23:21:12 prefetch.2.10.7: 1) 'SRR849745' was downloaded successfully Read 5198704 spots for SRR849745/SRR849745.sra Written 5198704 spots for SRR849745/SRR849745.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: 00:00:51 5198704 reads; of these: 5198704 (100.00%) were unpaired; of these: 152409 (2.93%) aligned 0 times 4194874 (80.69%) aligned exactly 1 time 851421 (16.38%) aligned >1 times 97.07% overall alignment rate Time searching: 00:00:51 Overall time: 00:00:51 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] 325983 / 5046295 = 0.0646 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 08:23:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277069/SRX277069.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277069/SRX277069.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277069/SRX277069.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277069/SRX277069.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 08:23:41: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:23:41: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:23:46: 1000000 INFO @ Tue, 16 Jun 2020 08:23:51: 2000000 INFO @ Tue, 16 Jun 2020 08:23:56: 3000000 INFO @ Tue, 16 Jun 2020 08:24:00: 4000000 INFO @ Tue, 16 Jun 2020 08:24:04: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:24:04: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:24:04: #1 total tags in treatment: 4720312 INFO @ Tue, 16 Jun 2020 08:24:04: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:24:04: #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 08:24:04: #1 tags after filtering in treatment: 4720312 INFO @ Tue, 16 Jun 2020 08:24:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:24:04: #1 finished! INFO @ Tue, 16 Jun 2020 08:24:04: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:24:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:24:04: #2 number of paired peaks: 396 WARNING @ Tue, 16 Jun 2020 08:24:04: Fewer paired peaks (396) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 396 pairs to build model! INFO @ Tue, 16 Jun 2020 08:24:04: start model_add_line... INFO @ Tue, 16 Jun 2020 08:24:04: start X-correlation... INFO @ Tue, 16 Jun 2020 08:24:04: end of X-cor INFO @ Tue, 16 Jun 2020 08:24:04: #2 finished! INFO @ Tue, 16 Jun 2020 08:24:04: #2 predicted fragment length is 33 bps INFO @ Tue, 16 Jun 2020 08:24:04: #2 alternative fragment length(s) may be 3,33,438,549,573 bps INFO @ Tue, 16 Jun 2020 08:24:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277069/SRX277069.05_model.r WARNING @ Tue, 16 Jun 2020 08:24:04: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:24:04: #2 You may need to consider one of the other alternative d(s): 3,33,438,549,573 WARNING @ Tue, 16 Jun 2020 08:24:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:24:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:24:04: #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 08:24:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277069/SRX277069.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277069/SRX277069.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277069/SRX277069.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277069/SRX277069.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 08:24:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:24:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:24:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:24:16: 1000000 INFO @ Tue, 16 Jun 2020 08:24:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277069/SRX277069.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:24:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277069/SRX277069.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:24:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277069/SRX277069.05_summits.bed INFO @ Tue, 16 Jun 2020 08:24:20: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (448 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:24:21: 2000000 INFO @ Tue, 16 Jun 2020 08:24:26: 3000000 INFO @ Tue, 16 Jun 2020 08:24:31: 4000000 INFO @ Tue, 16 Jun 2020 08:24:34: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:24:34: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:24:34: #1 total tags in treatment: 4720312 INFO @ Tue, 16 Jun 2020 08:24:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:24:34: #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 08:24:34: #1 tags after filtering in treatment: 4720312 INFO @ Tue, 16 Jun 2020 08:24:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:24:34: #1 finished! INFO @ Tue, 16 Jun 2020 08:24:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:24:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:24:35: #2 number of paired peaks: 396 WARNING @ Tue, 16 Jun 2020 08:24:35: Fewer paired peaks (396) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 396 pairs to build model! INFO @ Tue, 16 Jun 2020 08:24:35: start model_add_line... INFO @ Tue, 16 Jun 2020 08:24:35: start X-correlation... INFO @ Tue, 16 Jun 2020 08:24:35: end of X-cor INFO @ Tue, 16 Jun 2020 08:24:35: #2 finished! INFO @ Tue, 16 Jun 2020 08:24:35: #2 predicted fragment length is 33 bps INFO @ Tue, 16 Jun 2020 08:24:35: #2 alternative fragment length(s) may be 3,33,438,549,573 bps INFO @ Tue, 16 Jun 2020 08:24:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277069/SRX277069.10_model.r WARNING @ Tue, 16 Jun 2020 08:24:35: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:24:35: #2 You may need to consider one of the other alternative d(s): 3,33,438,549,573 WARNING @ Tue, 16 Jun 2020 08:24:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:24:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:24:35: #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 08:24:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277069/SRX277069.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277069/SRX277069.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277069/SRX277069.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277069/SRX277069.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 08:24:41: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:24:41: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:24:45: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:24:46: 1000000 INFO @ Tue, 16 Jun 2020 08:24:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277069/SRX277069.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:24:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277069/SRX277069.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:24:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277069/SRX277069.10_summits.bed INFO @ Tue, 16 Jun 2020 08:24:50: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (226 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:24:51: 2000000 INFO @ Tue, 16 Jun 2020 08:24:56: 3000000 INFO @ Tue, 16 Jun 2020 08:25:01: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:25:05: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:25:05: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:25:05: #1 total tags in treatment: 4720312 INFO @ Tue, 16 Jun 2020 08:25:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:25:05: #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 08:25:05: #1 tags after filtering in treatment: 4720312 INFO @ Tue, 16 Jun 2020 08:25:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:25:05: #1 finished! INFO @ Tue, 16 Jun 2020 08:25:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:25:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:25:06: #2 number of paired peaks: 396 WARNING @ Tue, 16 Jun 2020 08:25:06: Fewer paired peaks (396) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 396 pairs to build model! INFO @ Tue, 16 Jun 2020 08:25:06: start model_add_line... INFO @ Tue, 16 Jun 2020 08:25:06: start X-correlation... INFO @ Tue, 16 Jun 2020 08:25:06: end of X-cor INFO @ Tue, 16 Jun 2020 08:25:06: #2 finished! INFO @ Tue, 16 Jun 2020 08:25:06: #2 predicted fragment length is 33 bps INFO @ Tue, 16 Jun 2020 08:25:06: #2 alternative fragment length(s) may be 3,33,438,549,573 bps INFO @ Tue, 16 Jun 2020 08:25:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277069/SRX277069.20_model.r WARNING @ Tue, 16 Jun 2020 08:25:06: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:25:06: #2 You may need to consider one of the other alternative d(s): 3,33,438,549,573 WARNING @ Tue, 16 Jun 2020 08:25:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:25:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:25:06: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:25:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:25:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277069/SRX277069.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:25:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277069/SRX277069.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:25:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277069/SRX277069.20_summits.bed INFO @ Tue, 16 Jun 2020 08:25:21: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (63 records, 4 fields): 1 millis CompletedMACS2peakCalling