Job ID = 14160606 SRX = SRX9567199 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 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: 00:26:14 13328720 reads; of these: 13328720 (100.00%) were paired; of these: 6695746 (50.24%) aligned concordantly 0 times 5931144 (44.50%) aligned concordantly exactly 1 time 701830 (5.27%) aligned concordantly >1 times ---- 6695746 pairs aligned concordantly 0 times; of these: 5190284 (77.52%) aligned discordantly 1 time ---- 1505462 pairs aligned 0 times concordantly or discordantly; of these: 3010924 mates make up the pairs; of these: 892403 (29.64%) aligned 0 times 987686 (32.80%) aligned exactly 1 time 1130835 (37.56%) aligned >1 times 96.65% overall alignment rate Time searching: 00:26:14 Overall time: 00:26:14 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] 7969923 / 11818228 = 0.6744 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 03:57:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9567199/SRX9567199.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9567199/SRX9567199.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9567199/SRX9567199.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9567199/SRX9567199.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 03:57:03: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:57:03: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:57:09: 1000000 INFO @ Thu, 09 Dec 2021 03:57:16: 2000000 INFO @ Thu, 09 Dec 2021 03:57:23: 3000000 INFO @ Thu, 09 Dec 2021 03:57:30: 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 03:57:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9567199/SRX9567199.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9567199/SRX9567199.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9567199/SRX9567199.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9567199/SRX9567199.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 03:57:33: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:57:33: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:57:38: 5000000 INFO @ Thu, 09 Dec 2021 03:57:43: 1000000 INFO @ Thu, 09 Dec 2021 03:57:47: 6000000 INFO @ Thu, 09 Dec 2021 03:57:53: 2000000 INFO @ Thu, 09 Dec 2021 03:57:55: 7000000 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 03:58:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9567199/SRX9567199.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9567199/SRX9567199.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9567199/SRX9567199.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9567199/SRX9567199.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 03:58:03: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:58:03: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:58:04: 8000000 INFO @ Thu, 09 Dec 2021 03:58:04: 3000000 INFO @ Thu, 09 Dec 2021 03:58:12: 9000000 INFO @ Thu, 09 Dec 2021 03:58:13: 1000000 INFO @ Thu, 09 Dec 2021 03:58:15: 4000000 INFO @ Thu, 09 Dec 2021 03:58:20: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 03:58:20: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 03:58:20: #1 total tags in treatment: 2162212 INFO @ Thu, 09 Dec 2021 03:58:20: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:58:20: #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 03:58:20: #1 tags after filtering in treatment: 2053968 INFO @ Thu, 09 Dec 2021 03:58:20: #1 Redundant rate of treatment: 0.05 INFO @ Thu, 09 Dec 2021 03:58:20: #1 finished! INFO @ Thu, 09 Dec 2021 03:58:20: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:58:20: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:58:20: #2 number of paired peaks: 2421 INFO @ Thu, 09 Dec 2021 03:58:20: start model_add_line... INFO @ Thu, 09 Dec 2021 03:58:20: start X-correlation... INFO @ Thu, 09 Dec 2021 03:58:20: end of X-cor INFO @ Thu, 09 Dec 2021 03:58:20: #2 finished! INFO @ Thu, 09 Dec 2021 03:58:20: #2 predicted fragment length is 292 bps INFO @ Thu, 09 Dec 2021 03:58:20: #2 alternative fragment length(s) may be 292 bps INFO @ Thu, 09 Dec 2021 03:58:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9567199/SRX9567199.05_model.r WARNING @ Thu, 09 Dec 2021 03:58:20: #2 Since the d (292) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:58:20: #2 You may need to consider one of the other alternative d(s): 292 WARNING @ Thu, 09 Dec 2021 03:58:20: #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 03:58:20: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:58:20: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:58:24: 2000000 INFO @ Thu, 09 Dec 2021 03:58:25: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:58:26: 5000000 INFO @ Thu, 09 Dec 2021 03:58:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9567199/SRX9567199.05_peaks.xls INFO @ Thu, 09 Dec 2021 03:58:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9567199/SRX9567199.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:58:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9567199/SRX9567199.05_summits.bed INFO @ Thu, 09 Dec 2021 03:58:28: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1680 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:58:35: 3000000 INFO @ Thu, 09 Dec 2021 03:58:36: 6000000 INFO @ Thu, 09 Dec 2021 03:58:45: 4000000 INFO @ Thu, 09 Dec 2021 03:58:47: 7000000 INFO @ Thu, 09 Dec 2021 03:58:56: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 03:58:58: 8000000 INFO @ Thu, 09 Dec 2021 03:59:07: 6000000 INFO @ Thu, 09 Dec 2021 03:59:08: 9000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 03:59:17: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 03:59:17: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 03:59:17: #1 total tags in treatment: 2162212 INFO @ Thu, 09 Dec 2021 03:59:17: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:59:17: #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 03:59:17: #1 tags after filtering in treatment: 2053968 INFO @ Thu, 09 Dec 2021 03:59:17: #1 Redundant rate of treatment: 0.05 INFO @ Thu, 09 Dec 2021 03:59:17: #1 finished! INFO @ Thu, 09 Dec 2021 03:59:17: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:59:17: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:59:17: 7000000 INFO @ Thu, 09 Dec 2021 03:59:17: #2 number of paired peaks: 2421 INFO @ Thu, 09 Dec 2021 03:59:17: start model_add_line... INFO @ Thu, 09 Dec 2021 03:59:17: start X-correlation... INFO @ Thu, 09 Dec 2021 03:59:17: end of X-cor INFO @ Thu, 09 Dec 2021 03:59:17: #2 finished! INFO @ Thu, 09 Dec 2021 03:59:17: #2 predicted fragment length is 292 bps INFO @ Thu, 09 Dec 2021 03:59:17: #2 alternative fragment length(s) may be 292 bps INFO @ Thu, 09 Dec 2021 03:59:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9567199/SRX9567199.10_model.r WARNING @ Thu, 09 Dec 2021 03:59:17: #2 Since the d (292) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:59:17: #2 You may need to consider one of the other alternative d(s): 292 WARNING @ Thu, 09 Dec 2021 03:59:17: #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 03:59:17: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:59:17: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:59:23: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:59:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9567199/SRX9567199.10_peaks.xls INFO @ Thu, 09 Dec 2021 03:59:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9567199/SRX9567199.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:59:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9567199/SRX9567199.10_summits.bed INFO @ Thu, 09 Dec 2021 03:59:26: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (804 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:59:27: 8000000 INFO @ Thu, 09 Dec 2021 03:59:36: 9000000 INFO @ Thu, 09 Dec 2021 03:59:44: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 03:59:44: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 03:59:44: #1 total tags in treatment: 2162212 INFO @ Thu, 09 Dec 2021 03:59:44: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:59:44: #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 03:59:44: #1 tags after filtering in treatment: 2053968 INFO @ Thu, 09 Dec 2021 03:59:44: #1 Redundant rate of treatment: 0.05 INFO @ Thu, 09 Dec 2021 03:59:44: #1 finished! INFO @ Thu, 09 Dec 2021 03:59:44: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:59:44: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:59:44: #2 number of paired peaks: 2421 INFO @ Thu, 09 Dec 2021 03:59:44: start model_add_line... INFO @ Thu, 09 Dec 2021 03:59:44: start X-correlation... INFO @ Thu, 09 Dec 2021 03:59:44: end of X-cor INFO @ Thu, 09 Dec 2021 03:59:44: #2 finished! INFO @ Thu, 09 Dec 2021 03:59:44: #2 predicted fragment length is 292 bps INFO @ Thu, 09 Dec 2021 03:59:44: #2 alternative fragment length(s) may be 292 bps INFO @ Thu, 09 Dec 2021 03:59:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9567199/SRX9567199.20_model.r WARNING @ Thu, 09 Dec 2021 03:59:44: #2 Since the d (292) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:59:44: #2 You may need to consider one of the other alternative d(s): 292 WARNING @ Thu, 09 Dec 2021 03:59:44: #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 03:59:44: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:59:44: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:59:50: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:59:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9567199/SRX9567199.20_peaks.xls INFO @ Thu, 09 Dec 2021 03:59:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9567199/SRX9567199.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:59:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9567199/SRX9567199.20_summits.bed INFO @ Thu, 09 Dec 2021 03:59:53: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (355 records, 4 fields): 1 millis CompletedMACS2peakCalling