Job ID = 6626375 SRX = SRX7262213 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 15261138 spots for SRR10581836/SRR10581836.sra Written 15261138 spots for SRR10581836/SRR10581836.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626493 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:48 15261138 reads; of these: 15261138 (100.00%) were unpaired; of these: 4823627 (31.61%) aligned 0 times 7727290 (50.63%) aligned exactly 1 time 2710221 (17.76%) aligned >1 times 68.39% overall alignment rate Time searching: 00:02:48 Overall time: 00:02:48 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] 2324026 / 10437511 = 0.2227 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, 14 Jul 2020 07:02:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262213/SRX7262213.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262213/SRX7262213.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262213/SRX7262213.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262213/SRX7262213.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, 14 Jul 2020 07:02:50: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:02:50: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:02:55: 1000000 INFO @ Tue, 14 Jul 2020 07:03:01: 2000000 INFO @ Tue, 14 Jul 2020 07:03:06: 3000000 INFO @ Tue, 14 Jul 2020 07:03:11: 4000000 INFO @ Tue, 14 Jul 2020 07:03:17: 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, 14 Jul 2020 07:03:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262213/SRX7262213.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262213/SRX7262213.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262213/SRX7262213.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262213/SRX7262213.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, 14 Jul 2020 07:03:20: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:03:20: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:03:23: 6000000 INFO @ Tue, 14 Jul 2020 07:03:27: 1000000 INFO @ Tue, 14 Jul 2020 07:03:29: 7000000 INFO @ Tue, 14 Jul 2020 07:03:34: 2000000 INFO @ Tue, 14 Jul 2020 07:03:35: 8000000 INFO @ Tue, 14 Jul 2020 07:03:36: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:03:36: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:03:36: #1 total tags in treatment: 8113485 INFO @ Tue, 14 Jul 2020 07:03:36: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:03:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:03:36: #1 tags after filtering in treatment: 8113485 INFO @ Tue, 14 Jul 2020 07:03:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:03:36: #1 finished! INFO @ Tue, 14 Jul 2020 07:03:36: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:03:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:03:37: #2 number of paired peaks: 1238 INFO @ Tue, 14 Jul 2020 07:03:37: start model_add_line... INFO @ Tue, 14 Jul 2020 07:03:37: start X-correlation... INFO @ Tue, 14 Jul 2020 07:03:37: end of X-cor INFO @ Tue, 14 Jul 2020 07:03:37: #2 finished! INFO @ Tue, 14 Jul 2020 07:03:37: #2 predicted fragment length is 82 bps INFO @ Tue, 14 Jul 2020 07:03:37: #2 alternative fragment length(s) may be 3,82 bps INFO @ Tue, 14 Jul 2020 07:03:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262213/SRX7262213.05_model.r WARNING @ Tue, 14 Jul 2020 07:03:37: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:03:37: #2 You may need to consider one of the other alternative d(s): 3,82 WARNING @ Tue, 14 Jul 2020 07:03:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:03:37: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:03:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:03:41: 3000000 INFO @ Tue, 14 Jul 2020 07:03:47: 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, 14 Jul 2020 07:03:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262213/SRX7262213.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262213/SRX7262213.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262213/SRX7262213.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262213/SRX7262213.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, 14 Jul 2020 07:03:50: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:03:50: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:03:54: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:03:54: 5000000 INFO @ Tue, 14 Jul 2020 07:03:57: 1000000 INFO @ Tue, 14 Jul 2020 07:04:02: 6000000 INFO @ Tue, 14 Jul 2020 07:04:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262213/SRX7262213.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:04:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262213/SRX7262213.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:04:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262213/SRX7262213.05_summits.bed INFO @ Tue, 14 Jul 2020 07:04:02: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1196 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:04:04: 2000000 INFO @ Tue, 14 Jul 2020 07:04:09: 7000000 INFO @ Tue, 14 Jul 2020 07:04:11: 3000000 INFO @ Tue, 14 Jul 2020 07:04:16: 8000000 INFO @ Tue, 14 Jul 2020 07:04:17: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:04:17: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:04:17: #1 total tags in treatment: 8113485 INFO @ Tue, 14 Jul 2020 07:04:17: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:04:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:04:17: #1 tags after filtering in treatment: 8113485 INFO @ Tue, 14 Jul 2020 07:04:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:04:17: #1 finished! INFO @ Tue, 14 Jul 2020 07:04:17: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:04:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:04:18: #2 number of paired peaks: 1238 INFO @ Tue, 14 Jul 2020 07:04:18: start model_add_line... INFO @ Tue, 14 Jul 2020 07:04:18: start X-correlation... INFO @ Tue, 14 Jul 2020 07:04:18: end of X-cor INFO @ Tue, 14 Jul 2020 07:04:18: #2 finished! INFO @ Tue, 14 Jul 2020 07:04:18: #2 predicted fragment length is 82 bps INFO @ Tue, 14 Jul 2020 07:04:18: #2 alternative fragment length(s) may be 3,82 bps INFO @ Tue, 14 Jul 2020 07:04:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262213/SRX7262213.10_model.r WARNING @ Tue, 14 Jul 2020 07:04:18: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:04:18: #2 You may need to consider one of the other alternative d(s): 3,82 WARNING @ Tue, 14 Jul 2020 07:04:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:04:18: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:04:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:04:18: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:04:25: 5000000 INFO @ Tue, 14 Jul 2020 07:04:32: 6000000 INFO @ Tue, 14 Jul 2020 07:04:34: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:04:38: 7000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:04:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262213/SRX7262213.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:04:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262213/SRX7262213.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:04:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262213/SRX7262213.10_summits.bed INFO @ Tue, 14 Jul 2020 07:04:42: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (483 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:04:45: 8000000 INFO @ Tue, 14 Jul 2020 07:04:46: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:04:46: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:04:46: #1 total tags in treatment: 8113485 INFO @ Tue, 14 Jul 2020 07:04:46: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:04:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:04:46: #1 tags after filtering in treatment: 8113485 INFO @ Tue, 14 Jul 2020 07:04:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:04:46: #1 finished! INFO @ Tue, 14 Jul 2020 07:04:46: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:04:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:04:46: #2 number of paired peaks: 1238 INFO @ Tue, 14 Jul 2020 07:04:46: start model_add_line... INFO @ Tue, 14 Jul 2020 07:04:47: start X-correlation... INFO @ Tue, 14 Jul 2020 07:04:47: end of X-cor INFO @ Tue, 14 Jul 2020 07:04:47: #2 finished! INFO @ Tue, 14 Jul 2020 07:04:47: #2 predicted fragment length is 82 bps INFO @ Tue, 14 Jul 2020 07:04:47: #2 alternative fragment length(s) may be 3,82 bps INFO @ Tue, 14 Jul 2020 07:04:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262213/SRX7262213.20_model.r WARNING @ Tue, 14 Jul 2020 07:04:47: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:04:47: #2 You may need to consider one of the other alternative d(s): 3,82 WARNING @ Tue, 14 Jul 2020 07:04:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:04:47: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:04:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:05:03: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:05:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262213/SRX7262213.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:05:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262213/SRX7262213.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:05:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262213/SRX7262213.20_summits.bed INFO @ Tue, 14 Jul 2020 07:05:11: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (203 records, 4 fields): 15 millis CompletedMACS2peakCalling