Job ID = 14159931 SRX = SRX8845657 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: 00:05:55 6511885 reads; of these: 6511885 (100.00%) were paired; of these: 2389166 (36.69%) aligned concordantly 0 times 3451336 (53.00%) aligned concordantly exactly 1 time 671383 (10.31%) aligned concordantly >1 times ---- 2389166 pairs aligned concordantly 0 times; of these: 702546 (29.41%) aligned discordantly 1 time ---- 1686620 pairs aligned 0 times concordantly or discordantly; of these: 3373240 mates make up the pairs; of these: 2906345 (86.16%) aligned 0 times 193833 (5.75%) aligned exactly 1 time 273062 (8.09%) aligned >1 times 77.68% overall alignment rate Time searching: 00:05:55 Overall time: 00:05:55 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_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] 735753 / 4776708 = 0.1540 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 00:45:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8845657/SRX8845657.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8845657/SRX8845657.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8845657/SRX8845657.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8845657/SRX8845657.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 00:45:32: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:45:32: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:45:37: 1000000 INFO @ Thu, 09 Dec 2021 00:45:42: 2000000 INFO @ Thu, 09 Dec 2021 00:45:47: 3000000 INFO @ Thu, 09 Dec 2021 00:45:53: 4000000 INFO @ Thu, 09 Dec 2021 00:45:58: 5000000 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 00:46:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8845657/SRX8845657.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8845657/SRX8845657.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8845657/SRX8845657.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8845657/SRX8845657.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 00:46:02: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:46:02: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:46:03: 6000000 INFO @ Thu, 09 Dec 2021 00:46:07: 1000000 INFO @ Thu, 09 Dec 2021 00:46:08: 7000000 INFO @ Thu, 09 Dec 2021 00:46:13: 2000000 INFO @ Thu, 09 Dec 2021 00:46:13: 8000000 INFO @ Thu, 09 Dec 2021 00:46:17: #1 tag size is determined as 75 bps INFO @ Thu, 09 Dec 2021 00:46:17: #1 tag size = 75 INFO @ Thu, 09 Dec 2021 00:46:17: #1 total tags in treatment: 3494677 INFO @ Thu, 09 Dec 2021 00:46:17: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:46:17: #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 00:46:17: #1 tags after filtering in treatment: 2532532 INFO @ Thu, 09 Dec 2021 00:46:17: #1 Redundant rate of treatment: 0.28 INFO @ Thu, 09 Dec 2021 00:46:17: #1 finished! INFO @ Thu, 09 Dec 2021 00:46:17: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:46:17: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:46:17: #2 number of paired peaks: 3831 INFO @ Thu, 09 Dec 2021 00:46:17: start model_add_line... INFO @ Thu, 09 Dec 2021 00:46:17: start X-correlation... INFO @ Thu, 09 Dec 2021 00:46:17: end of X-cor INFO @ Thu, 09 Dec 2021 00:46:17: #2 finished! INFO @ Thu, 09 Dec 2021 00:46:17: #2 predicted fragment length is 115 bps INFO @ Thu, 09 Dec 2021 00:46:17: #2 alternative fragment length(s) may be 115 bps INFO @ Thu, 09 Dec 2021 00:46:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8845657/SRX8845657.05_model.r WARNING @ Thu, 09 Dec 2021 00:46:17: #2 Since the d (115) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 00:46:17: #2 You may need to consider one of the other alternative d(s): 115 WARNING @ Thu, 09 Dec 2021 00:46:17: #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 00:46:17: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:46:17: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:46:18: 3000000 INFO @ Thu, 09 Dec 2021 00:46:23: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:46:23: 4000000 INFO @ Thu, 09 Dec 2021 00:46:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8845657/SRX8845657.05_peaks.xls INFO @ Thu, 09 Dec 2021 00:46:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8845657/SRX8845657.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:46:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8845657/SRX8845657.05_summits.bed INFO @ Thu, 09 Dec 2021 00:46:26: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6750 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 00:46:28: 5000000 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 00:46:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8845657/SRX8845657.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8845657/SRX8845657.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8845657/SRX8845657.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8845657/SRX8845657.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 00:46:32: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:46:32: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:46:33: 6000000 INFO @ Thu, 09 Dec 2021 00:46:37: 1000000 INFO @ Thu, 09 Dec 2021 00:46:39: 7000000 INFO @ Thu, 09 Dec 2021 00:46:43: 2000000 INFO @ Thu, 09 Dec 2021 00:46:44: 8000000 INFO @ Thu, 09 Dec 2021 00:46:47: #1 tag size is determined as 75 bps INFO @ Thu, 09 Dec 2021 00:46:47: #1 tag size = 75 INFO @ Thu, 09 Dec 2021 00:46:47: #1 total tags in treatment: 3494677 INFO @ Thu, 09 Dec 2021 00:46:47: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:46:47: #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 00:46:48: #1 tags after filtering in treatment: 2532532 INFO @ Thu, 09 Dec 2021 00:46:48: #1 Redundant rate of treatment: 0.28 INFO @ Thu, 09 Dec 2021 00:46:48: #1 finished! INFO @ Thu, 09 Dec 2021 00:46:48: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:46:48: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:46:48: #2 number of paired peaks: 3831 INFO @ Thu, 09 Dec 2021 00:46:48: start model_add_line... INFO @ Thu, 09 Dec 2021 00:46:48: start X-correlation... INFO @ Thu, 09 Dec 2021 00:46:48: end of X-cor INFO @ Thu, 09 Dec 2021 00:46:48: #2 finished! INFO @ Thu, 09 Dec 2021 00:46:48: #2 predicted fragment length is 115 bps INFO @ Thu, 09 Dec 2021 00:46:48: #2 alternative fragment length(s) may be 115 bps INFO @ Thu, 09 Dec 2021 00:46:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8845657/SRX8845657.10_model.r WARNING @ Thu, 09 Dec 2021 00:46:48: #2 Since the d (115) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 00:46:48: #2 You may need to consider one of the other alternative d(s): 115 WARNING @ Thu, 09 Dec 2021 00:46:48: #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 00:46:48: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:46:48: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:46:48: 3000000 INFO @ Thu, 09 Dec 2021 00:46:53: 4000000 INFO @ Thu, 09 Dec 2021 00:46:53: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:46:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8845657/SRX8845657.10_peaks.xls INFO @ Thu, 09 Dec 2021 00:46:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8845657/SRX8845657.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:46:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8845657/SRX8845657.10_summits.bed INFO @ Thu, 09 Dec 2021 00:46:56: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4456 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 00:46:58: 5000000 INFO @ Thu, 09 Dec 2021 00:47:03: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 00:47:09: 7000000 INFO @ Thu, 09 Dec 2021 00:47:14: 8000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 00:47:17: #1 tag size is determined as 75 bps INFO @ Thu, 09 Dec 2021 00:47:17: #1 tag size = 75 INFO @ Thu, 09 Dec 2021 00:47:17: #1 total tags in treatment: 3494677 INFO @ Thu, 09 Dec 2021 00:47:17: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:47:17: #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 00:47:17: #1 tags after filtering in treatment: 2532532 INFO @ Thu, 09 Dec 2021 00:47:17: #1 Redundant rate of treatment: 0.28 INFO @ Thu, 09 Dec 2021 00:47:17: #1 finished! INFO @ Thu, 09 Dec 2021 00:47:17: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:47:17: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:47:18: #2 number of paired peaks: 3831 INFO @ Thu, 09 Dec 2021 00:47:18: start model_add_line... INFO @ Thu, 09 Dec 2021 00:47:18: start X-correlation... INFO @ Thu, 09 Dec 2021 00:47:18: end of X-cor INFO @ Thu, 09 Dec 2021 00:47:18: #2 finished! INFO @ Thu, 09 Dec 2021 00:47:18: #2 predicted fragment length is 115 bps INFO @ Thu, 09 Dec 2021 00:47:18: #2 alternative fragment length(s) may be 115 bps INFO @ Thu, 09 Dec 2021 00:47:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8845657/SRX8845657.20_model.r WARNING @ Thu, 09 Dec 2021 00:47:18: #2 Since the d (115) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 00:47:18: #2 You may need to consider one of the other alternative d(s): 115 WARNING @ Thu, 09 Dec 2021 00:47:18: #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 00:47:18: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:47:18: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:47:23: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:47:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8845657/SRX8845657.20_peaks.xls INFO @ Thu, 09 Dec 2021 00:47:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8845657/SRX8845657.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:47:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8845657/SRX8845657.20_summits.bed INFO @ Thu, 09 Dec 2021 00:47:26: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2345 records, 4 fields): 4 millis CompletedMACS2peakCalling