Job ID = 14159949 SRX = SRX8845652 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: 00:24:54 36116816 reads; of these: 36116816 (100.00%) were paired; of these: 15876571 (43.96%) aligned concordantly 0 times 17115360 (47.39%) aligned concordantly exactly 1 time 3124885 (8.65%) aligned concordantly >1 times ---- 15876571 pairs aligned concordantly 0 times; of these: 3160719 (19.91%) aligned discordantly 1 time ---- 12715852 pairs aligned 0 times concordantly or discordantly; of these: 25431704 mates make up the pairs; of these: 23182353 (91.16%) aligned 0 times 963094 (3.79%) aligned exactly 1 time 1286257 (5.06%) aligned >1 times 67.91% overall alignment rate Time searching: 00:24:54 Overall time: 00:24:54 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] 20618523 / 23192112 = 0.8890 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 01:17:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8845652/SRX8845652.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8845652/SRX8845652.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8845652/SRX8845652.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8845652/SRX8845652.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 01:17:13: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:17:13: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:17:21: 1000000 INFO @ Thu, 09 Dec 2021 01:17:29: 2000000 INFO @ Thu, 09 Dec 2021 01:17:36: 3000000 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 01:17:44: 4000000 INFO @ Thu, 09 Dec 2021 01:17:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8845652/SRX8845652.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8845652/SRX8845652.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8845652/SRX8845652.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8845652/SRX8845652.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 01:17:45: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:17:45: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:17:53: 5000000 INFO @ Thu, 09 Dec 2021 01:17:54: 1000000 INFO @ Thu, 09 Dec 2021 01:18:02: 6000000 INFO @ Thu, 09 Dec 2021 01:18:02: 2000000 INFO @ Thu, 09 Dec 2021 01:18:11: 7000000 INFO @ Thu, 09 Dec 2021 01:18:11: 3000000 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 01:18:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8845652/SRX8845652.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8845652/SRX8845652.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8845652/SRX8845652.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8845652/SRX8845652.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 01:18:13: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:18:13: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:18:18: #1 tag size is determined as 73 bps INFO @ Thu, 09 Dec 2021 01:18:18: #1 tag size = 73 INFO @ Thu, 09 Dec 2021 01:18:18: #1 total tags in treatment: 2084736 INFO @ Thu, 09 Dec 2021 01:18:18: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:18:18: #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 01:18:18: #1 tags after filtering in treatment: 1364583 INFO @ Thu, 09 Dec 2021 01:18:18: #1 Redundant rate of treatment: 0.35 INFO @ Thu, 09 Dec 2021 01:18:18: #1 finished! INFO @ Thu, 09 Dec 2021 01:18:18: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:18:18: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:18:18: #2 number of paired peaks: 3637 INFO @ Thu, 09 Dec 2021 01:18:18: start model_add_line... INFO @ Thu, 09 Dec 2021 01:18:18: start X-correlation... INFO @ Thu, 09 Dec 2021 01:18:18: end of X-cor INFO @ Thu, 09 Dec 2021 01:18:18: #2 finished! INFO @ Thu, 09 Dec 2021 01:18:18: #2 predicted fragment length is 113 bps INFO @ Thu, 09 Dec 2021 01:18:18: #2 alternative fragment length(s) may be 113 bps INFO @ Thu, 09 Dec 2021 01:18:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8845652/SRX8845652.05_model.r WARNING @ Thu, 09 Dec 2021 01:18:18: #2 Since the d (113) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 01:18:18: #2 You may need to consider one of the other alternative d(s): 113 WARNING @ Thu, 09 Dec 2021 01:18:18: #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 01:18:18: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:18:18: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:18:20: 4000000 INFO @ Thu, 09 Dec 2021 01:18:21: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 01:18:22: 1000000 INFO @ Thu, 09 Dec 2021 01:18:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8845652/SRX8845652.05_peaks.xls INFO @ Thu, 09 Dec 2021 01:18:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8845652/SRX8845652.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:18:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8845652/SRX8845652.05_summits.bed INFO @ Thu, 09 Dec 2021 01:18:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4520 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 01:18:28: 5000000 INFO @ Thu, 09 Dec 2021 01:18:30: 2000000 INFO @ Thu, 09 Dec 2021 01:18:36: 6000000 INFO @ Thu, 09 Dec 2021 01:18:39: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 01:18:45: 7000000 INFO @ Thu, 09 Dec 2021 01:18:48: 4000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 01:18:52: #1 tag size is determined as 73 bps INFO @ Thu, 09 Dec 2021 01:18:52: #1 tag size = 73 INFO @ Thu, 09 Dec 2021 01:18:52: #1 total tags in treatment: 2084736 INFO @ Thu, 09 Dec 2021 01:18:52: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:18:52: #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 01:18:52: #1 tags after filtering in treatment: 1364583 INFO @ Thu, 09 Dec 2021 01:18:52: #1 Redundant rate of treatment: 0.35 INFO @ Thu, 09 Dec 2021 01:18:52: #1 finished! INFO @ Thu, 09 Dec 2021 01:18:52: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:18:52: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:18:52: #2 number of paired peaks: 3637 INFO @ Thu, 09 Dec 2021 01:18:52: start model_add_line... INFO @ Thu, 09 Dec 2021 01:18:52: start X-correlation... INFO @ Thu, 09 Dec 2021 01:18:52: end of X-cor INFO @ Thu, 09 Dec 2021 01:18:52: #2 finished! INFO @ Thu, 09 Dec 2021 01:18:52: #2 predicted fragment length is 113 bps INFO @ Thu, 09 Dec 2021 01:18:52: #2 alternative fragment length(s) may be 113 bps INFO @ Thu, 09 Dec 2021 01:18:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8845652/SRX8845652.10_model.r WARNING @ Thu, 09 Dec 2021 01:18:52: #2 Since the d (113) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 01:18:52: #2 You may need to consider one of the other alternative d(s): 113 WARNING @ Thu, 09 Dec 2021 01:18:52: #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 01:18:52: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:18:52: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:18:55: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 01:18:56: 5000000 INFO @ Thu, 09 Dec 2021 01:18:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8845652/SRX8845652.10_peaks.xls INFO @ Thu, 09 Dec 2021 01:18:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8845652/SRX8845652.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:18:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8845652/SRX8845652.10_summits.bed INFO @ Thu, 09 Dec 2021 01:18:57: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2589 records, 4 fields): 57 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 01:19:03: 6000000 INFO @ Thu, 09 Dec 2021 01:19:11: 7000000 INFO @ Thu, 09 Dec 2021 01:19:17: #1 tag size is determined as 73 bps INFO @ Thu, 09 Dec 2021 01:19:17: #1 tag size = 73 INFO @ Thu, 09 Dec 2021 01:19:17: #1 total tags in treatment: 2084736 INFO @ Thu, 09 Dec 2021 01:19:17: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:19:17: #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 01:19:17: #1 tags after filtering in treatment: 1364583 INFO @ Thu, 09 Dec 2021 01:19:17: #1 Redundant rate of treatment: 0.35 INFO @ Thu, 09 Dec 2021 01:19:17: #1 finished! INFO @ Thu, 09 Dec 2021 01:19:17: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:19:17: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:19:17: #2 number of paired peaks: 3637 INFO @ Thu, 09 Dec 2021 01:19:17: start model_add_line... INFO @ Thu, 09 Dec 2021 01:19:17: start X-correlation... INFO @ Thu, 09 Dec 2021 01:19:17: end of X-cor INFO @ Thu, 09 Dec 2021 01:19:17: #2 finished! INFO @ Thu, 09 Dec 2021 01:19:17: #2 predicted fragment length is 113 bps INFO @ Thu, 09 Dec 2021 01:19:17: #2 alternative fragment length(s) may be 113 bps INFO @ Thu, 09 Dec 2021 01:19:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8845652/SRX8845652.20_model.r WARNING @ Thu, 09 Dec 2021 01:19:17: #2 Since the d (113) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 01:19:17: #2 You may need to consider one of the other alternative d(s): 113 WARNING @ Thu, 09 Dec 2021 01:19:17: #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 01:19:17: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:19:17: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:19:21: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 01:19:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8845652/SRX8845652.20_peaks.xls INFO @ Thu, 09 Dec 2021 01:19:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8845652/SRX8845652.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:19:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8845652/SRX8845652.20_summits.bed INFO @ Thu, 09 Dec 2021 01:19:22: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1088 records, 4 fields): 2 millis CompletedMACS2peakCalling