Job ID = 6368210 SRX = SRX494893 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:06:16 prefetch.2.10.7: 1) Downloading 'SRR1198425'... 2020-06-16T00:06:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:08:07 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:08:07 prefetch.2.10.7: 1) 'SRR1198425' was downloaded successfully Read 17571930 spots for SRR1198425/SRR1198425.sra Written 17571930 spots for SRR1198425/SRR1198425.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: 00:03:49 17571930 reads; of these: 17571930 (100.00%) were unpaired; of these: 2346783 (13.36%) aligned 0 times 12210437 (69.49%) aligned exactly 1 time 3014710 (17.16%) aligned >1 times 86.64% overall alignment rate Time searching: 00:03:49 Overall time: 00:03:49 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] 11448493 / 15225147 = 0.7519 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 09:15:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494893/SRX494893.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494893/SRX494893.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494893/SRX494893.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494893/SRX494893.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 09:15:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:15:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:15:43: 1000000 INFO @ Tue, 16 Jun 2020 09:15:50: 2000000 INFO @ Tue, 16 Jun 2020 09:15:57: 3000000 INFO @ Tue, 16 Jun 2020 09:16:02: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:16:02: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:16:02: #1 total tags in treatment: 3776654 INFO @ Tue, 16 Jun 2020 09:16:02: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:16:02: #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 09:16:02: #1 tags after filtering in treatment: 3776654 INFO @ Tue, 16 Jun 2020 09:16:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:16:02: #1 finished! INFO @ Tue, 16 Jun 2020 09:16:02: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:16:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:16:02: #2 number of paired peaks: 1111 INFO @ Tue, 16 Jun 2020 09:16:02: start model_add_line... INFO @ Tue, 16 Jun 2020 09:16:02: start X-correlation... INFO @ Tue, 16 Jun 2020 09:16:02: end of X-cor INFO @ Tue, 16 Jun 2020 09:16:02: #2 finished! INFO @ Tue, 16 Jun 2020 09:16:02: #2 predicted fragment length is 58 bps INFO @ Tue, 16 Jun 2020 09:16:02: #2 alternative fragment length(s) may be 58 bps INFO @ Tue, 16 Jun 2020 09:16:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494893/SRX494893.05_model.r WARNING @ Tue, 16 Jun 2020 09:16:02: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:16:02: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Tue, 16 Jun 2020 09:16:02: #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 09:16:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:16:02: #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 09:16:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494893/SRX494893.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494893/SRX494893.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494893/SRX494893.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494893/SRX494893.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 09:16:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:16:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:16:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:16:14: 1000000 INFO @ Tue, 16 Jun 2020 09:16:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494893/SRX494893.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:16:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494893/SRX494893.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:16:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494893/SRX494893.05_summits.bed INFO @ Tue, 16 Jun 2020 09:16:15: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1729 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:16:20: 2000000 INFO @ Tue, 16 Jun 2020 09:16:27: 3000000 INFO @ Tue, 16 Jun 2020 09:16:32: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:16:32: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:16:32: #1 total tags in treatment: 3776654 INFO @ Tue, 16 Jun 2020 09:16:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:16:32: #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 09:16:32: #1 tags after filtering in treatment: 3776654 INFO @ Tue, 16 Jun 2020 09:16:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:16:32: #1 finished! INFO @ Tue, 16 Jun 2020 09:16:32: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:16:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:16:33: #2 number of paired peaks: 1111 INFO @ Tue, 16 Jun 2020 09:16:33: start model_add_line... INFO @ Tue, 16 Jun 2020 09:16:33: start X-correlation... INFO @ Tue, 16 Jun 2020 09:16:33: end of X-cor INFO @ Tue, 16 Jun 2020 09:16:33: #2 finished! INFO @ Tue, 16 Jun 2020 09:16:33: #2 predicted fragment length is 58 bps INFO @ Tue, 16 Jun 2020 09:16:33: #2 alternative fragment length(s) may be 58 bps INFO @ Tue, 16 Jun 2020 09:16:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494893/SRX494893.10_model.r WARNING @ Tue, 16 Jun 2020 09:16:33: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:16:33: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Tue, 16 Jun 2020 09:16:33: #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 09:16:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:16:33: #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 09:16:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494893/SRX494893.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494893/SRX494893.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494893/SRX494893.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494893/SRX494893.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 09:16:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:16:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:16:41: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:16:44: 1000000 INFO @ Tue, 16 Jun 2020 09:16:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494893/SRX494893.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:16:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494893/SRX494893.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:16:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494893/SRX494893.10_summits.bed INFO @ Tue, 16 Jun 2020 09:16:46: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (895 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:16:51: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:16:58: 3000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:17:03: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:17:03: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:17:03: #1 total tags in treatment: 3776654 INFO @ Tue, 16 Jun 2020 09:17:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:17:03: #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 09:17:03: #1 tags after filtering in treatment: 3776654 INFO @ Tue, 16 Jun 2020 09:17:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:17:03: #1 finished! INFO @ Tue, 16 Jun 2020 09:17:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:17:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:17:03: #2 number of paired peaks: 1111 INFO @ Tue, 16 Jun 2020 09:17:03: start model_add_line... INFO @ Tue, 16 Jun 2020 09:17:03: start X-correlation... INFO @ Tue, 16 Jun 2020 09:17:03: end of X-cor INFO @ Tue, 16 Jun 2020 09:17:03: #2 finished! INFO @ Tue, 16 Jun 2020 09:17:03: #2 predicted fragment length is 58 bps INFO @ Tue, 16 Jun 2020 09:17:03: #2 alternative fragment length(s) may be 58 bps INFO @ Tue, 16 Jun 2020 09:17:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494893/SRX494893.20_model.r WARNING @ Tue, 16 Jun 2020 09:17:03: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:17:03: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Tue, 16 Jun 2020 09:17:03: #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 09:17:03: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:17:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:17:12: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:17:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494893/SRX494893.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:17:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494893/SRX494893.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:17:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494893/SRX494893.20_summits.bed INFO @ Tue, 16 Jun 2020 09:17:17: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (375 records, 4 fields): 2 millis CompletedMACS2peakCalling