Job ID = 8070519 SRX = SRX8392424 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: 00:16:12 10299312 reads; of these: 10299312 (100.00%) were paired; of these: 4466424 (43.37%) aligned concordantly 0 times 4922791 (47.80%) aligned concordantly exactly 1 time 910097 (8.84%) aligned concordantly >1 times ---- 4466424 pairs aligned concordantly 0 times; of these: 1212954 (27.16%) aligned discordantly 1 time ---- 3253470 pairs aligned 0 times concordantly or discordantly; of these: 6506940 mates make up the pairs; of these: 6071481 (93.31%) aligned 0 times 201051 (3.09%) aligned exactly 1 time 234408 (3.60%) aligned >1 times 70.52% overall alignment rate Time searching: 00:16:12 Overall time: 00:16:12 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] 1435490 / 6979777 = 0.2057 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 13:29:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8392424/SRX8392424.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8392424/SRX8392424.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8392424/SRX8392424.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8392424/SRX8392424.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 13:29:03: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:29:03: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:29:13: 1000000 INFO @ Sat, 08 Aug 2020 13:29:22: 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 13:29:32: 3000000 INFO @ Sat, 08 Aug 2020 13:29:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8392424/SRX8392424.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8392424/SRX8392424.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8392424/SRX8392424.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8392424/SRX8392424.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 13:29:33: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:29:33: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:29:44: 4000000 INFO @ Sat, 08 Aug 2020 13:29:45: 1000000 INFO @ Sat, 08 Aug 2020 13:29:55: 5000000 INFO @ Sat, 08 Aug 2020 13:29:56: 2000000 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 13:30:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8392424/SRX8392424.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8392424/SRX8392424.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8392424/SRX8392424.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8392424/SRX8392424.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 13:30:03: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:30:03: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:30:06: 6000000 INFO @ Sat, 08 Aug 2020 13:30:08: 3000000 INFO @ Sat, 08 Aug 2020 13:30:14: 1000000 INFO @ Sat, 08 Aug 2020 13:30:17: 7000000 INFO @ Sat, 08 Aug 2020 13:30:20: 4000000 INFO @ Sat, 08 Aug 2020 13:30:25: 2000000 INFO @ Sat, 08 Aug 2020 13:30:28: 8000000 INFO @ Sat, 08 Aug 2020 13:30:32: 5000000 INFO @ Sat, 08 Aug 2020 13:30:36: 3000000 INFO @ Sat, 08 Aug 2020 13:30:40: 9000000 INFO @ Sat, 08 Aug 2020 13:30:43: 6000000 INFO @ Sat, 08 Aug 2020 13:30:48: 4000000 INFO @ Sat, 08 Aug 2020 13:30:51: 10000000 INFO @ Sat, 08 Aug 2020 13:30:55: 7000000 INFO @ Sat, 08 Aug 2020 13:30:59: 5000000 INFO @ Sat, 08 Aug 2020 13:31:02: 11000000 INFO @ Sat, 08 Aug 2020 13:31:07: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 13:31:09: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:31:09: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:31:09: #1 total tags in treatment: 4600442 INFO @ Sat, 08 Aug 2020 13:31:09: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:31:09: #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 13:31:09: #1 tags after filtering in treatment: 4190620 INFO @ Sat, 08 Aug 2020 13:31:09: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 08 Aug 2020 13:31:09: #1 finished! INFO @ Sat, 08 Aug 2020 13:31:09: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:31:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:31:09: #2 number of paired peaks: 517 WARNING @ Sat, 08 Aug 2020 13:31:09: Fewer paired peaks (517) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 517 pairs to build model! INFO @ Sat, 08 Aug 2020 13:31:09: start model_add_line... INFO @ Sat, 08 Aug 2020 13:31:09: start X-correlation... INFO @ Sat, 08 Aug 2020 13:31:10: end of X-cor INFO @ Sat, 08 Aug 2020 13:31:10: #2 finished! INFO @ Sat, 08 Aug 2020 13:31:10: #2 predicted fragment length is 199 bps INFO @ Sat, 08 Aug 2020 13:31:10: #2 alternative fragment length(s) may be 199 bps INFO @ Sat, 08 Aug 2020 13:31:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8392424/SRX8392424.05_model.r WARNING @ Sat, 08 Aug 2020 13:31:10: #2 Since the d (199) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:31:10: #2 You may need to consider one of the other alternative d(s): 199 WARNING @ Sat, 08 Aug 2020 13:31:10: #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 13:31:10: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:31:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:31:10: 6000000 INFO @ Sat, 08 Aug 2020 13:31:19: 9000000 INFO @ Sat, 08 Aug 2020 13:31:19: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:31:21: 7000000 INFO @ Sat, 08 Aug 2020 13:31:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8392424/SRX8392424.05_peaks.xls INFO @ Sat, 08 Aug 2020 13:31:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8392424/SRX8392424.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:31:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8392424/SRX8392424.05_summits.bed INFO @ Sat, 08 Aug 2020 13:31:24: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (558 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:31:29: 10000000 BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 13:31:33: 8000000 INFO @ Sat, 08 Aug 2020 13:31:41: 11000000 INFO @ Sat, 08 Aug 2020 13:31:44: 9000000 INFO @ Sat, 08 Aug 2020 13:31:48: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:31:48: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:31:48: #1 total tags in treatment: 4600442 INFO @ Sat, 08 Aug 2020 13:31:48: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:31:48: #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 13:31:48: #1 tags after filtering in treatment: 4190620 INFO @ Sat, 08 Aug 2020 13:31:48: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 08 Aug 2020 13:31:48: #1 finished! INFO @ Sat, 08 Aug 2020 13:31:48: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:31:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:31:48: #2 number of paired peaks: 517 WARNING @ Sat, 08 Aug 2020 13:31:48: Fewer paired peaks (517) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 517 pairs to build model! INFO @ Sat, 08 Aug 2020 13:31:48: start model_add_line... INFO @ Sat, 08 Aug 2020 13:31:48: start X-correlation... INFO @ Sat, 08 Aug 2020 13:31:48: end of X-cor INFO @ Sat, 08 Aug 2020 13:31:48: #2 finished! INFO @ Sat, 08 Aug 2020 13:31:48: #2 predicted fragment length is 199 bps INFO @ Sat, 08 Aug 2020 13:31:48: #2 alternative fragment length(s) may be 199 bps INFO @ Sat, 08 Aug 2020 13:31:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8392424/SRX8392424.10_model.r WARNING @ Sat, 08 Aug 2020 13:31:48: #2 Since the d (199) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:31:48: #2 You may need to consider one of the other alternative d(s): 199 WARNING @ Sat, 08 Aug 2020 13:31:48: #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 13:31:48: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:31:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:31:54: 10000000 INFO @ Sat, 08 Aug 2020 13:31:58: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:32:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8392424/SRX8392424.10_peaks.xls INFO @ Sat, 08 Aug 2020 13:32:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8392424/SRX8392424.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:32:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8392424/SRX8392424.10_summits.bed INFO @ Sat, 08 Aug 2020 13:32:03: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (303 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:32:04: 11000000 INFO @ Sat, 08 Aug 2020 13:32:11: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:32:11: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:32:11: #1 total tags in treatment: 4600442 INFO @ Sat, 08 Aug 2020 13:32:11: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:32:11: #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 13:32:11: #1 tags after filtering in treatment: 4190620 INFO @ Sat, 08 Aug 2020 13:32:11: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 08 Aug 2020 13:32:11: #1 finished! INFO @ Sat, 08 Aug 2020 13:32:11: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:32:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:32:11: #2 number of paired peaks: 517 WARNING @ Sat, 08 Aug 2020 13:32:11: Fewer paired peaks (517) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 517 pairs to build model! INFO @ Sat, 08 Aug 2020 13:32:11: start model_add_line... INFO @ Sat, 08 Aug 2020 13:32:11: start X-correlation... INFO @ Sat, 08 Aug 2020 13:32:11: end of X-cor INFO @ Sat, 08 Aug 2020 13:32:11: #2 finished! INFO @ Sat, 08 Aug 2020 13:32:11: #2 predicted fragment length is 199 bps INFO @ Sat, 08 Aug 2020 13:32:11: #2 alternative fragment length(s) may be 199 bps INFO @ Sat, 08 Aug 2020 13:32:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8392424/SRX8392424.20_model.r WARNING @ Sat, 08 Aug 2020 13:32:11: #2 Since the d (199) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:32:11: #2 You may need to consider one of the other alternative d(s): 199 WARNING @ Sat, 08 Aug 2020 13:32:11: #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 13:32:11: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:32:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:32:21: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:32:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8392424/SRX8392424.20_peaks.xls INFO @ Sat, 08 Aug 2020 13:32:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8392424/SRX8392424.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:32:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8392424/SRX8392424.20_summits.bed INFO @ Sat, 08 Aug 2020 13:32:26: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (204 records, 4 fields): 1 millis CompletedMACS2peakCalling