Job ID = 8070289 SRX = SRX8392423 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: 00:12:16 7307015 reads; of these: 7307015 (100.00%) were paired; of these: 2209125 (30.23%) aligned concordantly 0 times 4373394 (59.85%) aligned concordantly exactly 1 time 724496 (9.92%) aligned concordantly >1 times ---- 2209125 pairs aligned concordantly 0 times; of these: 771129 (34.91%) aligned discordantly 1 time ---- 1437996 pairs aligned 0 times concordantly or discordantly; of these: 2875992 mates make up the pairs; of these: 2629796 (91.44%) aligned 0 times 106244 (3.69%) aligned exactly 1 time 139952 (4.87%) aligned >1 times 82.00% overall alignment rate Time searching: 00:12:16 Overall time: 00:12:16 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] 1096020 / 5822521 = 0.1882 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 13:19:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8392423/SRX8392423.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8392423/SRX8392423.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8392423/SRX8392423.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8392423/SRX8392423.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 13:19:43: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:19:43: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:19:53: 1000000 INFO @ Sat, 08 Aug 2020 13:20:02: 2000000 INFO @ Sat, 08 Aug 2020 13:20:11: 3000000 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 13:20:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8392423/SRX8392423.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8392423/SRX8392423.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8392423/SRX8392423.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8392423/SRX8392423.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 13:20:13: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:20:13: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:20:20: 4000000 INFO @ Sat, 08 Aug 2020 13:20:23: 1000000 INFO @ Sat, 08 Aug 2020 13:20:30: 5000000 INFO @ Sat, 08 Aug 2020 13:20:33: 2000000 INFO @ Sat, 08 Aug 2020 13:20:40: 6000000 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 13:20:43: 3000000 INFO @ Sat, 08 Aug 2020 13:20:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8392423/SRX8392423.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8392423/SRX8392423.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8392423/SRX8392423.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8392423/SRX8392423.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 13:20:44: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:20:44: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:20:50: 7000000 INFO @ Sat, 08 Aug 2020 13:20:53: 4000000 INFO @ Sat, 08 Aug 2020 13:20:54: 1000000 INFO @ Sat, 08 Aug 2020 13:21:00: 8000000 INFO @ Sat, 08 Aug 2020 13:21:02: 5000000 INFO @ Sat, 08 Aug 2020 13:21:04: 2000000 INFO @ Sat, 08 Aug 2020 13:21:10: 9000000 INFO @ Sat, 08 Aug 2020 13:21:12: 6000000 INFO @ Sat, 08 Aug 2020 13:21:14: 3000000 INFO @ Sat, 08 Aug 2020 13:21:18: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:21:18: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:21:18: #1 total tags in treatment: 4113575 INFO @ Sat, 08 Aug 2020 13:21:18: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:21:18: #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 13:21:18: #1 tags after filtering in treatment: 3840540 INFO @ Sat, 08 Aug 2020 13:21:18: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 08 Aug 2020 13:21:18: #1 finished! INFO @ Sat, 08 Aug 2020 13:21:18: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:21:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:21:19: #2 number of paired peaks: 456 WARNING @ Sat, 08 Aug 2020 13:21:19: Fewer paired peaks (456) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 456 pairs to build model! INFO @ Sat, 08 Aug 2020 13:21:19: start model_add_line... INFO @ Sat, 08 Aug 2020 13:21:19: start X-correlation... INFO @ Sat, 08 Aug 2020 13:21:19: end of X-cor INFO @ Sat, 08 Aug 2020 13:21:19: #2 finished! INFO @ Sat, 08 Aug 2020 13:21:19: #2 predicted fragment length is 206 bps INFO @ Sat, 08 Aug 2020 13:21:19: #2 alternative fragment length(s) may be 206 bps INFO @ Sat, 08 Aug 2020 13:21:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8392423/SRX8392423.05_model.r WARNING @ Sat, 08 Aug 2020 13:21:19: #2 Since the d (206) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:21:19: #2 You may need to consider one of the other alternative d(s): 206 WARNING @ Sat, 08 Aug 2020 13:21:19: #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 13:21:19: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:21:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:21:22: 7000000 INFO @ Sat, 08 Aug 2020 13:21:24: 4000000 INFO @ Sat, 08 Aug 2020 13:21:27: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:21:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8392423/SRX8392423.05_peaks.xls INFO @ Sat, 08 Aug 2020 13:21:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8392423/SRX8392423.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:21:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8392423/SRX8392423.05_summits.bed INFO @ Sat, 08 Aug 2020 13:21:31: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (341 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:21:32: 8000000 INFO @ Sat, 08 Aug 2020 13:21:33: 5000000 INFO @ Sat, 08 Aug 2020 13:21:43: 9000000 INFO @ Sat, 08 Aug 2020 13:21:43: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 13:21:50: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:21:50: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:21:50: #1 total tags in treatment: 4113575 INFO @ Sat, 08 Aug 2020 13:21:50: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:21:50: #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 13:21:51: #1 tags after filtering in treatment: 3840540 INFO @ Sat, 08 Aug 2020 13:21:51: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 08 Aug 2020 13:21:51: #1 finished! INFO @ Sat, 08 Aug 2020 13:21:51: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:21:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:21:51: #2 number of paired peaks: 456 WARNING @ Sat, 08 Aug 2020 13:21:51: Fewer paired peaks (456) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 456 pairs to build model! INFO @ Sat, 08 Aug 2020 13:21:51: start model_add_line... INFO @ Sat, 08 Aug 2020 13:21:51: start X-correlation... INFO @ Sat, 08 Aug 2020 13:21:51: end of X-cor INFO @ Sat, 08 Aug 2020 13:21:51: #2 finished! INFO @ Sat, 08 Aug 2020 13:21:51: #2 predicted fragment length is 206 bps INFO @ Sat, 08 Aug 2020 13:21:51: #2 alternative fragment length(s) may be 206 bps INFO @ Sat, 08 Aug 2020 13:21:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8392423/SRX8392423.10_model.r WARNING @ Sat, 08 Aug 2020 13:21:51: #2 Since the d (206) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:21:51: #2 You may need to consider one of the other alternative d(s): 206 WARNING @ Sat, 08 Aug 2020 13:21:51: #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 13:21:51: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:21:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:21:53: 7000000 INFO @ Sat, 08 Aug 2020 13:22:00: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:22:02: 8000000 INFO @ Sat, 08 Aug 2020 13:22:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8392423/SRX8392423.10_peaks.xls INFO @ Sat, 08 Aug 2020 13:22:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8392423/SRX8392423.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:22:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8392423/SRX8392423.10_summits.bed INFO @ Sat, 08 Aug 2020 13:22:04: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (246 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 13:22:11: 9000000 INFO @ Sat, 08 Aug 2020 13:22:18: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:22:18: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:22:18: #1 total tags in treatment: 4113575 INFO @ Sat, 08 Aug 2020 13:22:18: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:22:18: #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 13:22:18: #1 tags after filtering in treatment: 3840540 INFO @ Sat, 08 Aug 2020 13:22:18: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 08 Aug 2020 13:22:18: #1 finished! INFO @ Sat, 08 Aug 2020 13:22:18: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:22:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:22:18: #2 number of paired peaks: 456 WARNING @ Sat, 08 Aug 2020 13:22:18: Fewer paired peaks (456) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 456 pairs to build model! INFO @ Sat, 08 Aug 2020 13:22:18: start model_add_line... INFO @ Sat, 08 Aug 2020 13:22:19: start X-correlation... INFO @ Sat, 08 Aug 2020 13:22:19: end of X-cor INFO @ Sat, 08 Aug 2020 13:22:19: #2 finished! INFO @ Sat, 08 Aug 2020 13:22:19: #2 predicted fragment length is 206 bps INFO @ Sat, 08 Aug 2020 13:22:19: #2 alternative fragment length(s) may be 206 bps INFO @ Sat, 08 Aug 2020 13:22:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8392423/SRX8392423.20_model.r WARNING @ Sat, 08 Aug 2020 13:22:19: #2 Since the d (206) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:22:19: #2 You may need to consider one of the other alternative d(s): 206 WARNING @ Sat, 08 Aug 2020 13:22:19: #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 13:22:19: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:22:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:22:27: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:22:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8392423/SRX8392423.20_peaks.xls INFO @ Sat, 08 Aug 2020 13:22:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8392423/SRX8392423.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:22:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8392423/SRX8392423.20_summits.bed INFO @ Sat, 08 Aug 2020 13:22:31: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (164 records, 4 fields): 2 millis CompletedMACS2peakCalling