Job ID = 14160412 SRX = SRX9567191 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 13413645 spots for SRR13125166/SRR13125166.sra Written 13413645 spots for SRR13125166/SRR13125166.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160596 ("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: 00:25:04 13413645 reads; of these: 13413645 (100.00%) were paired; of these: 6054294 (45.14%) aligned concordantly 0 times 6535797 (48.72%) aligned concordantly exactly 1 time 823554 (6.14%) aligned concordantly >1 times ---- 6054294 pairs aligned concordantly 0 times; of these: 4487561 (74.12%) aligned discordantly 1 time ---- 1566733 pairs aligned 0 times concordantly or discordantly; of these: 3133466 mates make up the pairs; of these: 1317450 (42.04%) aligned 0 times 841867 (26.87%) aligned exactly 1 time 974149 (31.09%) aligned >1 times 95.09% overall alignment rate Time searching: 00:25:04 Overall time: 00:25:04 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 20 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 8698747 / 11842037 = 0.7346 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 02:49:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567191/SRX9567191.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567191/SRX9567191.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567191/SRX9567191.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567191/SRX9567191.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 @ Thu, 09 Dec 2021 02:49:08: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:49:08: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:49:15: 1000000 INFO @ Thu, 09 Dec 2021 02:49:21: 2000000 INFO @ Thu, 09 Dec 2021 02:49:28: 3000000 INFO @ Thu, 09 Dec 2021 02:49:35: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 02:49:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567191/SRX9567191.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567191/SRX9567191.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567191/SRX9567191.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567191/SRX9567191.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 @ Thu, 09 Dec 2021 02:49:38: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:49:38: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:49:42: 5000000 INFO @ Thu, 09 Dec 2021 02:49:45: 1000000 INFO @ Thu, 09 Dec 2021 02:49:49: 6000000 INFO @ Thu, 09 Dec 2021 02:49:53: 2000000 INFO @ Thu, 09 Dec 2021 02:49:57: 7000000 INFO @ Thu, 09 Dec 2021 02:50:01: 3000000 INFO @ Thu, 09 Dec 2021 02:50:05: 8000000 INFO @ Thu, 09 Dec 2021 02:50:06: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 02:50:06: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 02:50:06: #1 total tags in treatment: 1961963 INFO @ Thu, 09 Dec 2021 02:50:06: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:50:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 02:50:06: #1 tags after filtering in treatment: 1847574 INFO @ Thu, 09 Dec 2021 02:50:06: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 09 Dec 2021 02:50:06: #1 finished! INFO @ Thu, 09 Dec 2021 02:50:06: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:50:06: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:50:06: #2 number of paired peaks: 2044 INFO @ Thu, 09 Dec 2021 02:50:06: start model_add_line... INFO @ Thu, 09 Dec 2021 02:50:06: start X-correlation... INFO @ Thu, 09 Dec 2021 02:50:06: end of X-cor INFO @ Thu, 09 Dec 2021 02:50:06: #2 finished! INFO @ Thu, 09 Dec 2021 02:50:06: #2 predicted fragment length is 276 bps INFO @ Thu, 09 Dec 2021 02:50:06: #2 alternative fragment length(s) may be 276 bps INFO @ Thu, 09 Dec 2021 02:50:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567191/SRX9567191.05_model.r WARNING @ Thu, 09 Dec 2021 02:50:06: #2 Since the d (276) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 02:50:06: #2 You may need to consider one of the other alternative d(s): 276 WARNING @ Thu, 09 Dec 2021 02:50:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 02:50:06: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:50:06: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 02:50:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567191/SRX9567191.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567191/SRX9567191.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567191/SRX9567191.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567191/SRX9567191.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 @ Thu, 09 Dec 2021 02:50:08: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:50:08: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:50:08: 4000000 INFO @ Thu, 09 Dec 2021 02:50:11: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:50:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567191/SRX9567191.05_peaks.xls INFO @ Thu, 09 Dec 2021 02:50:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567191/SRX9567191.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:50:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567191/SRX9567191.05_summits.bed INFO @ Thu, 09 Dec 2021 02:50:13: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1417 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 02:50:16: 1000000 INFO @ Thu, 09 Dec 2021 02:50:16: 5000000 INFO @ Thu, 09 Dec 2021 02:50:24: 6000000 INFO @ Thu, 09 Dec 2021 02:50:24: 2000000 INFO @ Thu, 09 Dec 2021 02:50:32: 7000000 INFO @ Thu, 09 Dec 2021 02:50:32: 3000000 INFO @ Thu, 09 Dec 2021 02:50:40: 8000000 INFO @ Thu, 09 Dec 2021 02:50:40: 4000000 INFO @ Thu, 09 Dec 2021 02:50:41: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 02:50:41: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 02:50:41: #1 total tags in treatment: 1961963 INFO @ Thu, 09 Dec 2021 02:50:41: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:50:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 02:50:41: #1 tags after filtering in treatment: 1847574 INFO @ Thu, 09 Dec 2021 02:50:41: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 09 Dec 2021 02:50:41: #1 finished! INFO @ Thu, 09 Dec 2021 02:50:41: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:50:41: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:50:41: #2 number of paired peaks: 2044 INFO @ Thu, 09 Dec 2021 02:50:41: start model_add_line... INFO @ Thu, 09 Dec 2021 02:50:41: start X-correlation... INFO @ Thu, 09 Dec 2021 02:50:41: end of X-cor INFO @ Thu, 09 Dec 2021 02:50:41: #2 finished! INFO @ Thu, 09 Dec 2021 02:50:41: #2 predicted fragment length is 276 bps INFO @ Thu, 09 Dec 2021 02:50:41: #2 alternative fragment length(s) may be 276 bps INFO @ Thu, 09 Dec 2021 02:50:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567191/SRX9567191.10_model.r WARNING @ Thu, 09 Dec 2021 02:50:41: #2 Since the d (276) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 02:50:41: #2 You may need to consider one of the other alternative d(s): 276 WARNING @ Thu, 09 Dec 2021 02:50:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 02:50:41: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:50:41: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:50:46: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:50:48: 5000000 INFO @ Thu, 09 Dec 2021 02:50:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567191/SRX9567191.10_peaks.xls INFO @ Thu, 09 Dec 2021 02:50:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567191/SRX9567191.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:50:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567191/SRX9567191.10_summits.bed INFO @ Thu, 09 Dec 2021 02:50:48: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (683 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 02:50:55: 6000000 INFO @ Thu, 09 Dec 2021 02:51:03: 7000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 02:51:10: 8000000 INFO @ Thu, 09 Dec 2021 02:51:11: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 02:51:11: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 02:51:11: #1 total tags in treatment: 1961963 INFO @ Thu, 09 Dec 2021 02:51:11: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:51:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 02:51:11: #1 tags after filtering in treatment: 1847574 INFO @ Thu, 09 Dec 2021 02:51:11: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 09 Dec 2021 02:51:11: #1 finished! INFO @ Thu, 09 Dec 2021 02:51:11: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:51:11: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:51:11: #2 number of paired peaks: 2044 INFO @ Thu, 09 Dec 2021 02:51:11: start model_add_line... INFO @ Thu, 09 Dec 2021 02:51:11: start X-correlation... INFO @ Thu, 09 Dec 2021 02:51:11: end of X-cor INFO @ Thu, 09 Dec 2021 02:51:11: #2 finished! INFO @ Thu, 09 Dec 2021 02:51:11: #2 predicted fragment length is 276 bps INFO @ Thu, 09 Dec 2021 02:51:11: #2 alternative fragment length(s) may be 276 bps INFO @ Thu, 09 Dec 2021 02:51:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567191/SRX9567191.20_model.r WARNING @ Thu, 09 Dec 2021 02:51:11: #2 Since the d (276) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 02:51:11: #2 You may need to consider one of the other alternative d(s): 276 WARNING @ Thu, 09 Dec 2021 02:51:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 02:51:11: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:51:11: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:51:16: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:51:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567191/SRX9567191.20_peaks.xls INFO @ Thu, 09 Dec 2021 02:51:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567191/SRX9567191.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:51:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567191/SRX9567191.20_summits.bed INFO @ Thu, 09 Dec 2021 02:51:18: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (327 records, 4 fields): 2 millis CompletedMACS2peakCalling