Job ID = 8070354 SRX = SRX8392413 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: 00:14:35 8044827 reads; of these: 8044827 (100.00%) were paired; of these: 1970898 (24.50%) aligned concordantly 0 times 5156028 (64.09%) aligned concordantly exactly 1 time 917901 (11.41%) aligned concordantly >1 times ---- 1970898 pairs aligned concordantly 0 times; of these: 755229 (38.32%) aligned discordantly 1 time ---- 1215669 pairs aligned 0 times concordantly or discordantly; of these: 2431338 mates make up the pairs; of these: 2117136 (87.08%) aligned 0 times 159125 (6.54%) aligned exactly 1 time 155077 (6.38%) aligned >1 times 86.84% overall alignment rate Time searching: 00:14:35 Overall time: 00:14:35 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] 928487 / 6776903 = 0.1370 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 13:23:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8392413/SRX8392413.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8392413/SRX8392413.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8392413/SRX8392413.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8392413/SRX8392413.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 13:23:58: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:23:58: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:24:09: 1000000 INFO @ Sat, 08 Aug 2020 13:24:19: 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 13:24:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8392413/SRX8392413.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8392413/SRX8392413.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8392413/SRX8392413.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8392413/SRX8392413.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 13:24:28: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:24:28: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:24:30: 3000000 INFO @ Sat, 08 Aug 2020 13:24:39: 1000000 INFO @ Sat, 08 Aug 2020 13:24:42: 4000000 INFO @ Sat, 08 Aug 2020 13:24:49: 2000000 INFO @ Sat, 08 Aug 2020 13:24:54: 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 13:24:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8392413/SRX8392413.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8392413/SRX8392413.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8392413/SRX8392413.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8392413/SRX8392413.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 13:24:58: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:24:58: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:25:00: 3000000 INFO @ Sat, 08 Aug 2020 13:25:07: 6000000 INFO @ Sat, 08 Aug 2020 13:25:10: 1000000 INFO @ Sat, 08 Aug 2020 13:25:10: 4000000 INFO @ Sat, 08 Aug 2020 13:25:19: 7000000 INFO @ Sat, 08 Aug 2020 13:25:21: 5000000 INFO @ Sat, 08 Aug 2020 13:25:22: 2000000 INFO @ Sat, 08 Aug 2020 13:25:31: 8000000 INFO @ Sat, 08 Aug 2020 13:25:32: 6000000 INFO @ Sat, 08 Aug 2020 13:25:34: 3000000 INFO @ Sat, 08 Aug 2020 13:25:43: 7000000 INFO @ Sat, 08 Aug 2020 13:25:44: 9000000 INFO @ Sat, 08 Aug 2020 13:25:46: 4000000 INFO @ Sat, 08 Aug 2020 13:25:53: 8000000 INFO @ Sat, 08 Aug 2020 13:25:56: 10000000 INFO @ Sat, 08 Aug 2020 13:25:59: 5000000 INFO @ Sat, 08 Aug 2020 13:26:04: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 13:26:08: 11000000 INFO @ Sat, 08 Aug 2020 13:26:11: 6000000 INFO @ Sat, 08 Aug 2020 13:26:15: 10000000 INFO @ Sat, 08 Aug 2020 13:26:21: 12000000 INFO @ Sat, 08 Aug 2020 13:26:22: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:26:22: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:26:22: #1 total tags in treatment: 5225478 INFO @ Sat, 08 Aug 2020 13:26:22: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:26:22: #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 13:26:22: #1 tags after filtering in treatment: 4830802 INFO @ Sat, 08 Aug 2020 13:26:22: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 08 Aug 2020 13:26:22: #1 finished! INFO @ Sat, 08 Aug 2020 13:26:22: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:26:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:26:22: #2 number of paired peaks: 455 WARNING @ Sat, 08 Aug 2020 13:26:22: Fewer paired peaks (455) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 455 pairs to build model! INFO @ Sat, 08 Aug 2020 13:26:22: start model_add_line... INFO @ Sat, 08 Aug 2020 13:26:22: start X-correlation... INFO @ Sat, 08 Aug 2020 13:26:22: end of X-cor INFO @ Sat, 08 Aug 2020 13:26:22: #2 finished! INFO @ Sat, 08 Aug 2020 13:26:22: #2 predicted fragment length is 210 bps INFO @ Sat, 08 Aug 2020 13:26:22: #2 alternative fragment length(s) may be 210 bps INFO @ Sat, 08 Aug 2020 13:26:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8392413/SRX8392413.05_model.r WARNING @ Sat, 08 Aug 2020 13:26:22: #2 Since the d (210) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:26:22: #2 You may need to consider one of the other alternative d(s): 210 WARNING @ Sat, 08 Aug 2020 13:26:22: #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 13:26:22: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:26:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:26:24: 7000000 INFO @ Sat, 08 Aug 2020 13:26:25: 11000000 BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 13:26:33: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:26:36: 12000000 INFO @ Sat, 08 Aug 2020 13:26:36: 8000000 INFO @ Sat, 08 Aug 2020 13:26:37: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:26:37: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:26:37: #1 total tags in treatment: 5225478 INFO @ Sat, 08 Aug 2020 13:26:37: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:26:37: #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 13:26:37: #1 tags after filtering in treatment: 4830802 INFO @ Sat, 08 Aug 2020 13:26:37: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 08 Aug 2020 13:26:37: #1 finished! INFO @ Sat, 08 Aug 2020 13:26:37: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:26:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:26:37: #2 number of paired peaks: 455 WARNING @ Sat, 08 Aug 2020 13:26:37: Fewer paired peaks (455) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 455 pairs to build model! INFO @ Sat, 08 Aug 2020 13:26:37: start model_add_line... INFO @ Sat, 08 Aug 2020 13:26:37: start X-correlation... INFO @ Sat, 08 Aug 2020 13:26:37: end of X-cor INFO @ Sat, 08 Aug 2020 13:26:37: #2 finished! INFO @ Sat, 08 Aug 2020 13:26:37: #2 predicted fragment length is 210 bps INFO @ Sat, 08 Aug 2020 13:26:37: #2 alternative fragment length(s) may be 210 bps INFO @ Sat, 08 Aug 2020 13:26:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8392413/SRX8392413.10_model.r WARNING @ Sat, 08 Aug 2020 13:26:37: #2 Since the d (210) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:26:37: #2 You may need to consider one of the other alternative d(s): 210 WARNING @ Sat, 08 Aug 2020 13:26:37: #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 13:26:37: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:26:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:26:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8392413/SRX8392413.05_peaks.xls INFO @ Sat, 08 Aug 2020 13:26:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8392413/SRX8392413.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:26:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8392413/SRX8392413.05_summits.bed INFO @ Sat, 08 Aug 2020 13:26:38: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (337 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:26:47: 9000000 INFO @ Sat, 08 Aug 2020 13:26:48: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:26:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8392413/SRX8392413.10_peaks.xls INFO @ Sat, 08 Aug 2020 13:26:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8392413/SRX8392413.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:26:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8392413/SRX8392413.10_summits.bed INFO @ Sat, 08 Aug 2020 13:26:53: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (253 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:26:58: 10000000 INFO @ Sat, 08 Aug 2020 13:27:09: 11000000 INFO @ Sat, 08 Aug 2020 13:27:20: 12000000 INFO @ Sat, 08 Aug 2020 13:27:21: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:27:21: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:27:21: #1 total tags in treatment: 5225478 INFO @ Sat, 08 Aug 2020 13:27:21: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:27:21: #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 13:27:21: #1 tags after filtering in treatment: 4830802 INFO @ Sat, 08 Aug 2020 13:27:21: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 08 Aug 2020 13:27:21: #1 finished! INFO @ Sat, 08 Aug 2020 13:27:21: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:27:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:27:21: #2 number of paired peaks: 455 WARNING @ Sat, 08 Aug 2020 13:27:21: Fewer paired peaks (455) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 455 pairs to build model! INFO @ Sat, 08 Aug 2020 13:27:21: start model_add_line... INFO @ Sat, 08 Aug 2020 13:27:21: start X-correlation... INFO @ Sat, 08 Aug 2020 13:27:21: end of X-cor INFO @ Sat, 08 Aug 2020 13:27:21: #2 finished! INFO @ Sat, 08 Aug 2020 13:27:21: #2 predicted fragment length is 210 bps INFO @ Sat, 08 Aug 2020 13:27:21: #2 alternative fragment length(s) may be 210 bps INFO @ Sat, 08 Aug 2020 13:27:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8392413/SRX8392413.20_model.r WARNING @ Sat, 08 Aug 2020 13:27:21: #2 Since the d (210) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:27:21: #2 You may need to consider one of the other alternative d(s): 210 WARNING @ Sat, 08 Aug 2020 13:27:21: #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 13:27:21: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:27:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:27:32: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:27:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8392413/SRX8392413.20_peaks.xls INFO @ Sat, 08 Aug 2020 13:27:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8392413/SRX8392413.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:27:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8392413/SRX8392413.20_summits.bed INFO @ Sat, 08 Aug 2020 13:27:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (185 records, 4 fields): 3 millis CompletedMACS2peakCalling