Job ID = 14158204 SRX = SRX10641201 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: 00:23:31 18503562 reads; of these: 18503562 (100.00%) were paired; of these: 12615687 (68.18%) aligned concordantly 0 times 4048625 (21.88%) aligned concordantly exactly 1 time 1839250 (9.94%) aligned concordantly >1 times ---- 12615687 pairs aligned concordantly 0 times; of these: 1573233 (12.47%) aligned discordantly 1 time ---- 11042454 pairs aligned 0 times concordantly or discordantly; of these: 22084908 mates make up the pairs; of these: 21287591 (96.39%) aligned 0 times 436076 (1.97%) aligned exactly 1 time 361241 (1.64%) aligned >1 times 42.48% overall alignment rate Time searching: 00:23:31 Overall time: 00:23:31 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 12 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] 1330114 / 7424277 = 0.1792 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 @ Wed, 08 Dec 2021 15:19:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641201/SRX10641201.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641201/SRX10641201.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641201/SRX10641201.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641201/SRX10641201.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 @ Wed, 08 Dec 2021 15:19:48: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:19:48: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:19:57: 1000000 INFO @ Wed, 08 Dec 2021 15:20:08: 2000000 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 @ Wed, 08 Dec 2021 15:20:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641201/SRX10641201.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641201/SRX10641201.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641201/SRX10641201.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641201/SRX10641201.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 @ Wed, 08 Dec 2021 15:20:18: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:20:18: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:20:18: 3000000 INFO @ Wed, 08 Dec 2021 15:20:28: 1000000 INFO @ Wed, 08 Dec 2021 15:20:29: 4000000 INFO @ Wed, 08 Dec 2021 15:20:38: 2000000 INFO @ Wed, 08 Dec 2021 15:20:39: 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 @ Wed, 08 Dec 2021 15:20:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641201/SRX10641201.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641201/SRX10641201.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641201/SRX10641201.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641201/SRX10641201.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 @ Wed, 08 Dec 2021 15:20:48: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:20:48: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:20:48: 3000000 INFO @ Wed, 08 Dec 2021 15:20:49: 6000000 INFO @ Wed, 08 Dec 2021 15:20:58: 1000000 INFO @ Wed, 08 Dec 2021 15:20:59: 4000000 INFO @ Wed, 08 Dec 2021 15:21:00: 7000000 INFO @ Wed, 08 Dec 2021 15:21:09: 2000000 INFO @ Wed, 08 Dec 2021 15:21:09: 5000000 INFO @ Wed, 08 Dec 2021 15:21:10: 8000000 INFO @ Wed, 08 Dec 2021 15:21:19: 3000000 INFO @ Wed, 08 Dec 2021 15:21:20: 6000000 INFO @ Wed, 08 Dec 2021 15:21:21: 9000000 INFO @ Wed, 08 Dec 2021 15:21:30: 4000000 INFO @ Wed, 08 Dec 2021 15:21:30: 7000000 INFO @ Wed, 08 Dec 2021 15:21:31: 10000000 INFO @ Wed, 08 Dec 2021 15:21:40: 5000000 INFO @ Wed, 08 Dec 2021 15:21:40: 8000000 INFO @ Wed, 08 Dec 2021 15:21:42: 11000000 INFO @ Wed, 08 Dec 2021 15:21:51: 9000000 INFO @ Wed, 08 Dec 2021 15:21:51: 6000000 INFO @ Wed, 08 Dec 2021 15:21:52: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 15:22:01: 10000000 INFO @ Wed, 08 Dec 2021 15:22:01: 7000000 INFO @ Wed, 08 Dec 2021 15:22:03: 13000000 INFO @ Wed, 08 Dec 2021 15:22:03: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 15:22:03: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 15:22:03: #1 total tags in treatment: 4725014 INFO @ Wed, 08 Dec 2021 15:22:03: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 15:22:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 15:22:03: #1 tags after filtering in treatment: 3759326 INFO @ Wed, 08 Dec 2021 15:22:03: #1 Redundant rate of treatment: 0.20 INFO @ Wed, 08 Dec 2021 15:22:03: #1 finished! INFO @ Wed, 08 Dec 2021 15:22:03: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 15:22:03: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 15:22:04: #2 number of paired peaks: 1288 INFO @ Wed, 08 Dec 2021 15:22:04: start model_add_line... INFO @ Wed, 08 Dec 2021 15:22:04: start X-correlation... INFO @ Wed, 08 Dec 2021 15:22:04: end of X-cor INFO @ Wed, 08 Dec 2021 15:22:04: #2 finished! INFO @ Wed, 08 Dec 2021 15:22:04: #2 predicted fragment length is 252 bps INFO @ Wed, 08 Dec 2021 15:22:04: #2 alternative fragment length(s) may be 252 bps INFO @ Wed, 08 Dec 2021 15:22:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641201/SRX10641201.05_model.r WARNING @ Wed, 08 Dec 2021 15:22:04: #2 Since the d (252) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 15:22:04: #2 You may need to consider one of the other alternative d(s): 252 WARNING @ Wed, 08 Dec 2021 15:22:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 15:22:04: #3 Call peaks... INFO @ Wed, 08 Dec 2021 15:22:04: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 15:22:12: 11000000 INFO @ Wed, 08 Dec 2021 15:22:12: 8000000 INFO @ Wed, 08 Dec 2021 15:22:14: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 15:22:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641201/SRX10641201.05_peaks.xls INFO @ Wed, 08 Dec 2021 15:22:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641201/SRX10641201.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:22:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641201/SRX10641201.05_summits.bed INFO @ Wed, 08 Dec 2021 15:22:18: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2590 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 15:22:22: 12000000 INFO @ Wed, 08 Dec 2021 15:22:22: 9000000 INFO @ Wed, 08 Dec 2021 15:22:32: 13000000 INFO @ Wed, 08 Dec 2021 15:22:33: 10000000 INFO @ Wed, 08 Dec 2021 15:22:33: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 15:22:33: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 15:22:33: #1 total tags in treatment: 4725014 INFO @ Wed, 08 Dec 2021 15:22:33: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 15:22:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 15:22:33: #1 tags after filtering in treatment: 3759326 INFO @ Wed, 08 Dec 2021 15:22:33: #1 Redundant rate of treatment: 0.20 INFO @ Wed, 08 Dec 2021 15:22:33: #1 finished! INFO @ Wed, 08 Dec 2021 15:22:33: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 15:22:33: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 15:22:33: #2 number of paired peaks: 1288 INFO @ Wed, 08 Dec 2021 15:22:33: start model_add_line... INFO @ Wed, 08 Dec 2021 15:22:33: start X-correlation... INFO @ Wed, 08 Dec 2021 15:22:33: end of X-cor INFO @ Wed, 08 Dec 2021 15:22:33: #2 finished! INFO @ Wed, 08 Dec 2021 15:22:33: #2 predicted fragment length is 252 bps INFO @ Wed, 08 Dec 2021 15:22:33: #2 alternative fragment length(s) may be 252 bps INFO @ Wed, 08 Dec 2021 15:22:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641201/SRX10641201.10_model.r WARNING @ Wed, 08 Dec 2021 15:22:33: #2 Since the d (252) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 15:22:33: #2 You may need to consider one of the other alternative d(s): 252 WARNING @ Wed, 08 Dec 2021 15:22:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 15:22:33: #3 Call peaks... INFO @ Wed, 08 Dec 2021 15:22:33: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 15:22:42: 11000000 INFO @ Wed, 08 Dec 2021 15:22:43: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 15:22:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641201/SRX10641201.10_peaks.xls INFO @ Wed, 08 Dec 2021 15:22:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641201/SRX10641201.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:22:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641201/SRX10641201.10_summits.bed INFO @ Wed, 08 Dec 2021 15:22:47: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1409 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 15:22:52: 12000000 INFO @ Wed, 08 Dec 2021 15:23:01: 13000000 INFO @ Wed, 08 Dec 2021 15:23:02: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 15:23:02: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 15:23:02: #1 total tags in treatment: 4725014 INFO @ Wed, 08 Dec 2021 15:23:02: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 15:23:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 15:23:02: #1 tags after filtering in treatment: 3759326 INFO @ Wed, 08 Dec 2021 15:23:02: #1 Redundant rate of treatment: 0.20 INFO @ Wed, 08 Dec 2021 15:23:02: #1 finished! INFO @ Wed, 08 Dec 2021 15:23:02: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 15:23:02: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 15:23:02: #2 number of paired peaks: 1288 INFO @ Wed, 08 Dec 2021 15:23:02: start model_add_line... INFO @ Wed, 08 Dec 2021 15:23:02: start X-correlation... INFO @ Wed, 08 Dec 2021 15:23:02: end of X-cor INFO @ Wed, 08 Dec 2021 15:23:02: #2 finished! INFO @ Wed, 08 Dec 2021 15:23:02: #2 predicted fragment length is 252 bps INFO @ Wed, 08 Dec 2021 15:23:02: #2 alternative fragment length(s) may be 252 bps INFO @ Wed, 08 Dec 2021 15:23:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641201/SRX10641201.20_model.r WARNING @ Wed, 08 Dec 2021 15:23:02: #2 Since the d (252) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 15:23:02: #2 You may need to consider one of the other alternative d(s): 252 WARNING @ Wed, 08 Dec 2021 15:23:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 15:23:02: #3 Call peaks... INFO @ Wed, 08 Dec 2021 15:23:02: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 15:23:13: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 15:23:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641201/SRX10641201.20_peaks.xls INFO @ Wed, 08 Dec 2021 15:23:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641201/SRX10641201.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:23:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641201/SRX10641201.20_summits.bed INFO @ Wed, 08 Dec 2021 15:23:17: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (683 records, 4 fields): 2 millis CompletedMACS2peakCalling