Job ID = 8070394 SRX = SRX8392419 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: 00:14:21 8473861 reads; of these: 8473861 (100.00%) were paired; of these: 1554066 (18.34%) aligned concordantly 0 times 6159607 (72.69%) aligned concordantly exactly 1 time 760188 (8.97%) aligned concordantly >1 times ---- 1554066 pairs aligned concordantly 0 times; of these: 728403 (46.87%) aligned discordantly 1 time ---- 825663 pairs aligned 0 times concordantly or discordantly; of these: 1651326 mates make up the pairs; of these: 1418181 (85.88%) aligned 0 times 96880 (5.87%) aligned exactly 1 time 136265 (8.25%) aligned >1 times 91.63% overall alignment rate Time searching: 00:14:21 Overall time: 00:14:21 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] 1462845 / 7601283 = 0.1924 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 08 Aug 2020 13:24:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8392419/SRX8392419.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8392419/SRX8392419.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8392419/SRX8392419.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8392419/SRX8392419.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, 08 Aug 2020 13:24:33: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:24:33: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:24:43: 1000000 INFO @ Sat, 08 Aug 2020 13:24:53: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 08 Aug 2020 13:25:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8392419/SRX8392419.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8392419/SRX8392419.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8392419/SRX8392419.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8392419/SRX8392419.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, 08 Aug 2020 13:25:03: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:25:03: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:25:04: 3000000 INFO @ Sat, 08 Aug 2020 13:25:14: 1000000 INFO @ Sat, 08 Aug 2020 13:25:15: 4000000 INFO @ Sat, 08 Aug 2020 13:25:26: 2000000 INFO @ Sat, 08 Aug 2020 13:25:26: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 08 Aug 2020 13:25:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8392419/SRX8392419.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8392419/SRX8392419.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8392419/SRX8392419.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8392419/SRX8392419.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, 08 Aug 2020 13:25:33: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:25:33: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:25:38: 6000000 INFO @ Sat, 08 Aug 2020 13:25:38: 3000000 INFO @ Sat, 08 Aug 2020 13:25:43: 1000000 INFO @ Sat, 08 Aug 2020 13:25:49: 7000000 INFO @ Sat, 08 Aug 2020 13:25:50: 4000000 INFO @ Sat, 08 Aug 2020 13:25:53: 2000000 INFO @ Sat, 08 Aug 2020 13:26:01: 8000000 INFO @ Sat, 08 Aug 2020 13:26:01: 5000000 INFO @ Sat, 08 Aug 2020 13:26:04: 3000000 INFO @ Sat, 08 Aug 2020 13:26:12: 9000000 INFO @ Sat, 08 Aug 2020 13:26:13: 6000000 INFO @ Sat, 08 Aug 2020 13:26:14: 4000000 INFO @ Sat, 08 Aug 2020 13:26:24: 10000000 INFO @ Sat, 08 Aug 2020 13:26:24: 5000000 INFO @ Sat, 08 Aug 2020 13:26:25: 7000000 INFO @ Sat, 08 Aug 2020 13:26:35: 6000000 INFO @ Sat, 08 Aug 2020 13:26:35: 11000000 INFO @ Sat, 08 Aug 2020 13:26:37: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 13:26:45: 7000000 INFO @ Sat, 08 Aug 2020 13:26:46: 12000000 INFO @ Sat, 08 Aug 2020 13:26:49: 9000000 INFO @ Sat, 08 Aug 2020 13:26:53: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:26:53: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:26:53: #1 total tags in treatment: 5549515 INFO @ Sat, 08 Aug 2020 13:26:53: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:26:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 13:26:53: #1 tags after filtering in treatment: 4960532 INFO @ Sat, 08 Aug 2020 13:26:53: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 08 Aug 2020 13:26:53: #1 finished! INFO @ Sat, 08 Aug 2020 13:26:53: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:26:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:26:54: #2 number of paired peaks: 2051 INFO @ Sat, 08 Aug 2020 13:26:54: start model_add_line... INFO @ Sat, 08 Aug 2020 13:26:54: start X-correlation... INFO @ Sat, 08 Aug 2020 13:26:54: end of X-cor INFO @ Sat, 08 Aug 2020 13:26:54: #2 finished! INFO @ Sat, 08 Aug 2020 13:26:54: #2 predicted fragment length is 203 bps INFO @ Sat, 08 Aug 2020 13:26:54: #2 alternative fragment length(s) may be 203 bps INFO @ Sat, 08 Aug 2020 13:26:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8392419/SRX8392419.05_model.r WARNING @ Sat, 08 Aug 2020 13:26:54: #2 Since the d (203) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:26:54: #2 You may need to consider one of the other alternative d(s): 203 WARNING @ Sat, 08 Aug 2020 13:26:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 13:26:54: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:26:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:26:55: 8000000 INFO @ Sat, 08 Aug 2020 13:27:01: 10000000 BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 13:27:05: 9000000 INFO @ Sat, 08 Aug 2020 13:27:06: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:27:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8392419/SRX8392419.05_peaks.xls INFO @ Sat, 08 Aug 2020 13:27:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8392419/SRX8392419.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:27:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8392419/SRX8392419.05_summits.bed INFO @ Sat, 08 Aug 2020 13:27:12: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (7811 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:27:13: 11000000 INFO @ Sat, 08 Aug 2020 13:27:16: 10000000 INFO @ Sat, 08 Aug 2020 13:27:24: 12000000 INFO @ Sat, 08 Aug 2020 13:27:26: 11000000 INFO @ Sat, 08 Aug 2020 13:27:31: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:27:31: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:27:31: #1 total tags in treatment: 5549515 INFO @ Sat, 08 Aug 2020 13:27:31: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:27:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 13:27:31: #1 tags after filtering in treatment: 4960532 INFO @ Sat, 08 Aug 2020 13:27:31: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 08 Aug 2020 13:27:31: #1 finished! INFO @ Sat, 08 Aug 2020 13:27:31: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:27:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:27:32: #2 number of paired peaks: 2051 INFO @ Sat, 08 Aug 2020 13:27:32: start model_add_line... INFO @ Sat, 08 Aug 2020 13:27:32: start X-correlation... INFO @ Sat, 08 Aug 2020 13:27:32: end of X-cor INFO @ Sat, 08 Aug 2020 13:27:32: #2 finished! INFO @ Sat, 08 Aug 2020 13:27:32: #2 predicted fragment length is 203 bps INFO @ Sat, 08 Aug 2020 13:27:32: #2 alternative fragment length(s) may be 203 bps INFO @ Sat, 08 Aug 2020 13:27:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8392419/SRX8392419.10_model.r WARNING @ Sat, 08 Aug 2020 13:27:32: #2 Since the d (203) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:27:32: #2 You may need to consider one of the other alternative d(s): 203 WARNING @ Sat, 08 Aug 2020 13:27:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 13:27:32: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:27:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:27:36: 12000000 INFO @ Sat, 08 Aug 2020 13:27:42: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:27:42: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:27:42: #1 total tags in treatment: 5549515 INFO @ Sat, 08 Aug 2020 13:27:42: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:27:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 13:27:42: #1 tags after filtering in treatment: 4960532 INFO @ Sat, 08 Aug 2020 13:27:42: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 08 Aug 2020 13:27:42: #1 finished! INFO @ Sat, 08 Aug 2020 13:27:42: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:27:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:27:42: #2 number of paired peaks: 2051 INFO @ Sat, 08 Aug 2020 13:27:42: start model_add_line... INFO @ Sat, 08 Aug 2020 13:27:42: start X-correlation... INFO @ Sat, 08 Aug 2020 13:27:42: end of X-cor INFO @ Sat, 08 Aug 2020 13:27:42: #2 finished! INFO @ Sat, 08 Aug 2020 13:27:42: #2 predicted fragment length is 203 bps INFO @ Sat, 08 Aug 2020 13:27:42: #2 alternative fragment length(s) may be 203 bps INFO @ Sat, 08 Aug 2020 13:27:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8392419/SRX8392419.20_model.r WARNING @ Sat, 08 Aug 2020 13:27:42: #2 Since the d (203) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:27:42: #2 You may need to consider one of the other alternative d(s): 203 WARNING @ Sat, 08 Aug 2020 13:27:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 13:27:42: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:27:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:27:44: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:27:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8392419/SRX8392419.10_peaks.xls INFO @ Sat, 08 Aug 2020 13:27:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8392419/SRX8392419.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:27:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8392419/SRX8392419.10_summits.bed INFO @ Sat, 08 Aug 2020 13:27:50: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4953 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:27:54: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:27:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8392419/SRX8392419.20_peaks.xls INFO @ Sat, 08 Aug 2020 13:27:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8392419/SRX8392419.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:27:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8392419/SRX8392419.20_summits.bed INFO @ Sat, 08 Aug 2020 13:27:59: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2257 records, 4 fields): 4 millis CompletedMACS2peakCalling