Job ID = 14159935 SRX = SRX8845656 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: 00:06:38 6984741 reads; of these: 6984741 (100.00%) were paired; of these: 2245531 (32.15%) aligned concordantly 0 times 3935186 (56.34%) aligned concordantly exactly 1 time 804024 (11.51%) aligned concordantly >1 times ---- 2245531 pairs aligned concordantly 0 times; of these: 735616 (32.76%) aligned discordantly 1 time ---- 1509915 pairs aligned 0 times concordantly or discordantly; of these: 3019830 mates make up the pairs; of these: 2523883 (83.58%) aligned 0 times 208965 (6.92%) aligned exactly 1 time 286982 (9.50%) aligned >1 times 81.93% overall alignment rate Time searching: 00:06:38 Overall time: 00:06:38 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] 861078 / 5420227 = 0.1589 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 00:49:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8845656/SRX8845656.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8845656/SRX8845656.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8845656/SRX8845656.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8845656/SRX8845656.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 00:49:09: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:49:09: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:49:16: 1000000 INFO @ Thu, 09 Dec 2021 00:49:24: 2000000 INFO @ Thu, 09 Dec 2021 00:49:32: 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 00:49:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8845656/SRX8845656.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8845656/SRX8845656.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8845656/SRX8845656.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8845656/SRX8845656.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 00:49:39: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:49:39: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:49:40: 4000000 INFO @ Thu, 09 Dec 2021 00:49:48: 1000000 INFO @ Thu, 09 Dec 2021 00:49:50: 5000000 INFO @ Thu, 09 Dec 2021 00:49:57: 2000000 INFO @ Thu, 09 Dec 2021 00:49:59: 6000000 INFO @ Thu, 09 Dec 2021 00:50:06: 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 00:50:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8845656/SRX8845656.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8845656/SRX8845656.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8845656/SRX8845656.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8845656/SRX8845656.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 00:50:09: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:50:09: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:50:09: 7000000 INFO @ Thu, 09 Dec 2021 00:50:15: 4000000 INFO @ Thu, 09 Dec 2021 00:50:19: 8000000 INFO @ Thu, 09 Dec 2021 00:50:19: 1000000 INFO @ Thu, 09 Dec 2021 00:50:25: 5000000 INFO @ Thu, 09 Dec 2021 00:50:28: 9000000 INFO @ Thu, 09 Dec 2021 00:50:31: 2000000 INFO @ Thu, 09 Dec 2021 00:50:35: 6000000 INFO @ Thu, 09 Dec 2021 00:50:35: #1 tag size is determined as 75 bps INFO @ Thu, 09 Dec 2021 00:50:35: #1 tag size = 75 INFO @ Thu, 09 Dec 2021 00:50:35: #1 total tags in treatment: 3991902 INFO @ Thu, 09 Dec 2021 00:50:35: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:50:35: #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 00:50:35: #1 tags after filtering in treatment: 2939946 INFO @ Thu, 09 Dec 2021 00:50:35: #1 Redundant rate of treatment: 0.26 INFO @ Thu, 09 Dec 2021 00:50:35: #1 finished! INFO @ Thu, 09 Dec 2021 00:50:35: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:50:35: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:50:35: #2 number of paired peaks: 2948 INFO @ Thu, 09 Dec 2021 00:50:35: start model_add_line... INFO @ Thu, 09 Dec 2021 00:50:36: start X-correlation... INFO @ Thu, 09 Dec 2021 00:50:36: end of X-cor INFO @ Thu, 09 Dec 2021 00:50:36: #2 finished! INFO @ Thu, 09 Dec 2021 00:50:36: #2 predicted fragment length is 116 bps INFO @ Thu, 09 Dec 2021 00:50:36: #2 alternative fragment length(s) may be 116 bps INFO @ Thu, 09 Dec 2021 00:50:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8845656/SRX8845656.05_model.r WARNING @ Thu, 09 Dec 2021 00:50:36: #2 Since the d (116) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 00:50:36: #2 You may need to consider one of the other alternative d(s): 116 WARNING @ Thu, 09 Dec 2021 00:50:36: #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 00:50:36: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:50:36: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:50:39: 3000000 INFO @ Thu, 09 Dec 2021 00:50:42: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:50:44: 7000000 INFO @ Thu, 09 Dec 2021 00:50:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8845656/SRX8845656.05_peaks.xls INFO @ Thu, 09 Dec 2021 00:50:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8845656/SRX8845656.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:50:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8845656/SRX8845656.05_summits.bed INFO @ Thu, 09 Dec 2021 00:50:46: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6407 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 00:50:49: 4000000 INFO @ Thu, 09 Dec 2021 00:50:53: 8000000 INFO @ Thu, 09 Dec 2021 00:50:58: 5000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 00:51:03: 9000000 INFO @ Thu, 09 Dec 2021 00:51:08: 6000000 INFO @ Thu, 09 Dec 2021 00:51:09: #1 tag size is determined as 75 bps INFO @ Thu, 09 Dec 2021 00:51:09: #1 tag size = 75 INFO @ Thu, 09 Dec 2021 00:51:09: #1 total tags in treatment: 3991902 INFO @ Thu, 09 Dec 2021 00:51:09: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:51:09: #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 00:51:09: #1 tags after filtering in treatment: 2939946 INFO @ Thu, 09 Dec 2021 00:51:09: #1 Redundant rate of treatment: 0.26 INFO @ Thu, 09 Dec 2021 00:51:09: #1 finished! INFO @ Thu, 09 Dec 2021 00:51:09: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:51:09: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:51:10: #2 number of paired peaks: 2948 INFO @ Thu, 09 Dec 2021 00:51:10: start model_add_line... INFO @ Thu, 09 Dec 2021 00:51:10: start X-correlation... INFO @ Thu, 09 Dec 2021 00:51:10: end of X-cor INFO @ Thu, 09 Dec 2021 00:51:10: #2 finished! INFO @ Thu, 09 Dec 2021 00:51:10: #2 predicted fragment length is 116 bps INFO @ Thu, 09 Dec 2021 00:51:10: #2 alternative fragment length(s) may be 116 bps INFO @ Thu, 09 Dec 2021 00:51:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8845656/SRX8845656.10_model.r WARNING @ Thu, 09 Dec 2021 00:51:10: #2 Since the d (116) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 00:51:10: #2 You may need to consider one of the other alternative d(s): 116 WARNING @ Thu, 09 Dec 2021 00:51:10: #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 00:51:10: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:51:10: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:51:16: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:51:17: 7000000 INFO @ Thu, 09 Dec 2021 00:51:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8845656/SRX8845656.10_peaks.xls INFO @ Thu, 09 Dec 2021 00:51:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8845656/SRX8845656.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:51:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8845656/SRX8845656.10_summits.bed INFO @ Thu, 09 Dec 2021 00:51:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4074 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 00:51:25: 8000000 INFO @ Thu, 09 Dec 2021 00:51:33: 9000000 INFO @ Thu, 09 Dec 2021 00:51:39: #1 tag size is determined as 75 bps INFO @ Thu, 09 Dec 2021 00:51:39: #1 tag size = 75 INFO @ Thu, 09 Dec 2021 00:51:39: #1 total tags in treatment: 3991902 INFO @ Thu, 09 Dec 2021 00:51:39: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:51:39: #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 00:51:39: #1 tags after filtering in treatment: 2939946 INFO @ Thu, 09 Dec 2021 00:51:39: #1 Redundant rate of treatment: 0.26 INFO @ Thu, 09 Dec 2021 00:51:39: #1 finished! INFO @ Thu, 09 Dec 2021 00:51:39: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:51:39: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:51:40: #2 number of paired peaks: 2948 INFO @ Thu, 09 Dec 2021 00:51:40: start model_add_line... INFO @ Thu, 09 Dec 2021 00:51:40: start X-correlation... INFO @ Thu, 09 Dec 2021 00:51:40: end of X-cor INFO @ Thu, 09 Dec 2021 00:51:40: #2 finished! INFO @ Thu, 09 Dec 2021 00:51:40: #2 predicted fragment length is 116 bps INFO @ Thu, 09 Dec 2021 00:51:40: #2 alternative fragment length(s) may be 116 bps INFO @ Thu, 09 Dec 2021 00:51:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8845656/SRX8845656.20_model.r WARNING @ Thu, 09 Dec 2021 00:51:40: #2 Since the d (116) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 00:51:40: #2 You may need to consider one of the other alternative d(s): 116 WARNING @ Thu, 09 Dec 2021 00:51:40: #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 00:51:40: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:51:40: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:51:46: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:51:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8845656/SRX8845656.20_peaks.xls INFO @ Thu, 09 Dec 2021 00:51:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8845656/SRX8845656.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:51:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8845656/SRX8845656.20_summits.bed INFO @ Thu, 09 Dec 2021 00:51:50: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2244 records, 4 fields): 5 millis CompletedMACS2peakCalling