Job ID = 12265162 SRX = SRX2332999 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: 00:11:30 29523880 reads; of these: 29523880 (100.00%) were paired; of these: 27669491 (93.72%) aligned concordantly 0 times 1346432 (4.56%) aligned concordantly exactly 1 time 507957 (1.72%) aligned concordantly >1 times ---- 27669491 pairs aligned concordantly 0 times; of these: 308020 (1.11%) aligned discordantly 1 time ---- 27361471 pairs aligned 0 times concordantly or discordantly; of these: 54722942 mates make up the pairs; of these: 54466397 (99.53%) aligned 0 times 67109 (0.12%) aligned exactly 1 time 189436 (0.35%) aligned >1 times 7.76% overall alignment rate Time searching: 00:11:30 Overall time: 00:11:30 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_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] 553493 / 2149538 = 0.2575 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:24:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2332999/SRX2332999.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2332999/SRX2332999.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2332999/SRX2332999.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2332999/SRX2332999.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 @ Sat, 03 Apr 2021 06:24:56: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:24:56: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:25:05: 1000000 INFO @ Sat, 03 Apr 2021 06:25:14: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:25:24: 3000000 INFO @ Sat, 03 Apr 2021 06:25:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2332999/SRX2332999.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2332999/SRX2332999.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2332999/SRX2332999.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2332999/SRX2332999.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 @ Sat, 03 Apr 2021 06:25:26: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:25:26: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:25:28: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 06:25:28: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 06:25:28: #1 total tags in treatment: 1357142 INFO @ Sat, 03 Apr 2021 06:25:28: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:25:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:25:28: #1 tags after filtering in treatment: 1071390 INFO @ Sat, 03 Apr 2021 06:25:28: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 03 Apr 2021 06:25:28: #1 finished! INFO @ Sat, 03 Apr 2021 06:25:28: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:25:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:25:28: #2 number of paired peaks: 1088 INFO @ Sat, 03 Apr 2021 06:25:28: start model_add_line... INFO @ Sat, 03 Apr 2021 06:25:28: start X-correlation... INFO @ Sat, 03 Apr 2021 06:25:28: end of X-cor INFO @ Sat, 03 Apr 2021 06:25:28: #2 finished! INFO @ Sat, 03 Apr 2021 06:25:28: #2 predicted fragment length is 166 bps INFO @ Sat, 03 Apr 2021 06:25:28: #2 alternative fragment length(s) may be 166 bps INFO @ Sat, 03 Apr 2021 06:25:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2332999/SRX2332999.05_model.r WARNING @ Sat, 03 Apr 2021 06:25:29: #2 Since the d (166) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:25:29: #2 You may need to consider one of the other alternative d(s): 166 WARNING @ Sat, 03 Apr 2021 06:25:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:25:29: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:25:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:25:32: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:25:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2332999/SRX2332999.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:25:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2332999/SRX2332999.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:25:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2332999/SRX2332999.05_summits.bed INFO @ Sat, 03 Apr 2021 06:25:34: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (868 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:25:36: 1000000 INFO @ Sat, 03 Apr 2021 06:25:45: 2000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:25:55: 3000000 INFO @ Sat, 03 Apr 2021 06:25:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2332999/SRX2332999.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2332999/SRX2332999.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2332999/SRX2332999.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2332999/SRX2332999.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 @ Sat, 03 Apr 2021 06:25:56: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:25:56: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:26:00: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 06:26:00: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 06:26:00: #1 total tags in treatment: 1357142 INFO @ Sat, 03 Apr 2021 06:26:00: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:26:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:26:00: #1 tags after filtering in treatment: 1071390 INFO @ Sat, 03 Apr 2021 06:26:00: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 03 Apr 2021 06:26:00: #1 finished! INFO @ Sat, 03 Apr 2021 06:26:00: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:26:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:26:00: #2 number of paired peaks: 1088 INFO @ Sat, 03 Apr 2021 06:26:00: start model_add_line... INFO @ Sat, 03 Apr 2021 06:26:00: start X-correlation... INFO @ Sat, 03 Apr 2021 06:26:00: end of X-cor INFO @ Sat, 03 Apr 2021 06:26:00: #2 finished! INFO @ Sat, 03 Apr 2021 06:26:00: #2 predicted fragment length is 166 bps INFO @ Sat, 03 Apr 2021 06:26:00: #2 alternative fragment length(s) may be 166 bps INFO @ Sat, 03 Apr 2021 06:26:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2332999/SRX2332999.10_model.r WARNING @ Sat, 03 Apr 2021 06:26:00: #2 Since the d (166) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:26:00: #2 You may need to consider one of the other alternative d(s): 166 WARNING @ Sat, 03 Apr 2021 06:26:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:26:00: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:26:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:26:04: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:26:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2332999/SRX2332999.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:26:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2332999/SRX2332999.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:26:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2332999/SRX2332999.10_summits.bed INFO @ Sat, 03 Apr 2021 06:26:06: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (368 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:26:06: 1000000 INFO @ Sat, 03 Apr 2021 06:26:16: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:26:26: 3000000 INFO @ Sat, 03 Apr 2021 06:26:30: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 06:26:30: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 06:26:30: #1 total tags in treatment: 1357142 INFO @ Sat, 03 Apr 2021 06:26:30: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:26:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:26:30: #1 tags after filtering in treatment: 1071390 INFO @ Sat, 03 Apr 2021 06:26:30: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 03 Apr 2021 06:26:30: #1 finished! INFO @ Sat, 03 Apr 2021 06:26:30: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:26:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:26:30: #2 number of paired peaks: 1088 INFO @ Sat, 03 Apr 2021 06:26:30: start model_add_line... INFO @ Sat, 03 Apr 2021 06:26:30: start X-correlation... INFO @ Sat, 03 Apr 2021 06:26:30: end of X-cor INFO @ Sat, 03 Apr 2021 06:26:30: #2 finished! INFO @ Sat, 03 Apr 2021 06:26:30: #2 predicted fragment length is 166 bps INFO @ Sat, 03 Apr 2021 06:26:30: #2 alternative fragment length(s) may be 166 bps INFO @ Sat, 03 Apr 2021 06:26:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2332999/SRX2332999.20_model.r WARNING @ Sat, 03 Apr 2021 06:26:30: #2 Since the d (166) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:26:30: #2 You may need to consider one of the other alternative d(s): 166 WARNING @ Sat, 03 Apr 2021 06:26:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:26:30: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:26:30: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:26:34: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:26:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2332999/SRX2332999.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:26:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2332999/SRX2332999.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:26:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2332999/SRX2332999.20_summits.bed INFO @ Sat, 03 Apr 2021 06:26:36: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (128 records, 4 fields): 5 millis CompletedMACS2peakCalling