Job ID = 8070421 SRX = SRX8392422 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: 00:13:46 8452957 reads; of these: 8452957 (100.00%) were paired; of these: 2862873 (33.87%) aligned concordantly 0 times 4755042 (56.25%) aligned concordantly exactly 1 time 835042 (9.88%) aligned concordantly >1 times ---- 2862873 pairs aligned concordantly 0 times; of these: 948371 (33.13%) aligned discordantly 1 time ---- 1914502 pairs aligned 0 times concordantly or discordantly; of these: 3829004 mates make up the pairs; of these: 3503579 (91.50%) aligned 0 times 146152 (3.82%) aligned exactly 1 time 179273 (4.68%) aligned >1 times 79.28% overall alignment rate Time searching: 00:13:46 Overall time: 00:13:46 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] 1271704 / 6482957 = 0.1962 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 13:24:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8392422/SRX8392422.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8392422/SRX8392422.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8392422/SRX8392422.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8392422/SRX8392422.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 13:24:48: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:24:48: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:24:57: 1000000 INFO @ Sat, 08 Aug 2020 13:25:06: 2000000 INFO @ Sat, 08 Aug 2020 13:25:16: 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 13:25:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8392422/SRX8392422.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8392422/SRX8392422.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8392422/SRX8392422.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8392422/SRX8392422.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 13:25:18: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:25:18: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:25:26: 4000000 INFO @ Sat, 08 Aug 2020 13:25:26: 1000000 INFO @ Sat, 08 Aug 2020 13:25:35: 2000000 INFO @ Sat, 08 Aug 2020 13:25:36: 5000000 INFO @ Sat, 08 Aug 2020 13:25:44: 3000000 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 13:25:47: 6000000 INFO @ Sat, 08 Aug 2020 13:25:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8392422/SRX8392422.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8392422/SRX8392422.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8392422/SRX8392422.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8392422/SRX8392422.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 13:25:48: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:25:48: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:25:52: 4000000 INFO @ Sat, 08 Aug 2020 13:25:57: 7000000 INFO @ Sat, 08 Aug 2020 13:25:58: 1000000 INFO @ Sat, 08 Aug 2020 13:26:01: 5000000 INFO @ Sat, 08 Aug 2020 13:26:08: 8000000 INFO @ Sat, 08 Aug 2020 13:26:09: 2000000 INFO @ Sat, 08 Aug 2020 13:26:10: 6000000 INFO @ Sat, 08 Aug 2020 13:26:18: 9000000 INFO @ Sat, 08 Aug 2020 13:26:19: 7000000 INFO @ Sat, 08 Aug 2020 13:26:19: 3000000 INFO @ Sat, 08 Aug 2020 13:26:27: 8000000 INFO @ Sat, 08 Aug 2020 13:26:29: 10000000 INFO @ Sat, 08 Aug 2020 13:26:30: 4000000 INFO @ Sat, 08 Aug 2020 13:26:36: 9000000 INFO @ Sat, 08 Aug 2020 13:26:38: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:26:38: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:26:38: #1 total tags in treatment: 4465796 INFO @ Sat, 08 Aug 2020 13:26:38: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:26:38: #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 13:26:38: #1 tags after filtering in treatment: 4129757 INFO @ Sat, 08 Aug 2020 13:26:38: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 08 Aug 2020 13:26:38: #1 finished! INFO @ Sat, 08 Aug 2020 13:26:38: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:26:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:26:38: #2 number of paired peaks: 486 WARNING @ Sat, 08 Aug 2020 13:26:38: Fewer paired peaks (486) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 486 pairs to build model! INFO @ Sat, 08 Aug 2020 13:26:38: start model_add_line... INFO @ Sat, 08 Aug 2020 13:26:38: start X-correlation... INFO @ Sat, 08 Aug 2020 13:26:38: end of X-cor INFO @ Sat, 08 Aug 2020 13:26:38: #2 finished! INFO @ Sat, 08 Aug 2020 13:26:38: #2 predicted fragment length is 208 bps INFO @ Sat, 08 Aug 2020 13:26:38: #2 alternative fragment length(s) may be 208 bps INFO @ Sat, 08 Aug 2020 13:26:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8392422/SRX8392422.05_model.r WARNING @ Sat, 08 Aug 2020 13:26:38: #2 Since the d (208) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:26:38: #2 You may need to consider one of the other alternative d(s): 208 WARNING @ Sat, 08 Aug 2020 13:26:38: #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 13:26:38: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:26:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:26:40: 5000000 INFO @ Sat, 08 Aug 2020 13:26:45: 10000000 INFO @ Sat, 08 Aug 2020 13:26:48: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:26:50: 6000000 INFO @ Sat, 08 Aug 2020 13:26:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8392422/SRX8392422.05_peaks.xls INFO @ Sat, 08 Aug 2020 13:26:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8392422/SRX8392422.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:26:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8392422/SRX8392422.05_summits.bed INFO @ Sat, 08 Aug 2020 13:26:52: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (417 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:26:52: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:26:52: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:26:52: #1 total tags in treatment: 4465796 INFO @ Sat, 08 Aug 2020 13:26:52: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:26:52: #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 13:26:52: #1 tags after filtering in treatment: 4129757 INFO @ Sat, 08 Aug 2020 13:26:52: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 08 Aug 2020 13:26:52: #1 finished! INFO @ Sat, 08 Aug 2020 13:26:52: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:26:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:26:53: #2 number of paired peaks: 486 WARNING @ Sat, 08 Aug 2020 13:26:53: Fewer paired peaks (486) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 486 pairs to build model! INFO @ Sat, 08 Aug 2020 13:26:53: start model_add_line... INFO @ Sat, 08 Aug 2020 13:26:53: start X-correlation... INFO @ Sat, 08 Aug 2020 13:26:53: end of X-cor INFO @ Sat, 08 Aug 2020 13:26:53: #2 finished! INFO @ Sat, 08 Aug 2020 13:26:53: #2 predicted fragment length is 208 bps INFO @ Sat, 08 Aug 2020 13:26:53: #2 alternative fragment length(s) may be 208 bps INFO @ Sat, 08 Aug 2020 13:26:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8392422/SRX8392422.10_model.r WARNING @ Sat, 08 Aug 2020 13:26:53: #2 Since the d (208) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:26:53: #2 You may need to consider one of the other alternative d(s): 208 WARNING @ Sat, 08 Aug 2020 13:26:53: #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 13:26:53: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:26:53: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 13:27:00: 7000000 INFO @ Sat, 08 Aug 2020 13:27:02: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:27:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8392422/SRX8392422.10_peaks.xls INFO @ Sat, 08 Aug 2020 13:27:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8392422/SRX8392422.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:27:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8392422/SRX8392422.10_summits.bed INFO @ Sat, 08 Aug 2020 13:27:07: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (257 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:27:09: 8000000 BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 13:27:19: 9000000 INFO @ Sat, 08 Aug 2020 13:27:29: 10000000 INFO @ Sat, 08 Aug 2020 13:27:37: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:27:37: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:27:37: #1 total tags in treatment: 4465796 INFO @ Sat, 08 Aug 2020 13:27:37: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:27:37: #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 13:27:37: #1 tags after filtering in treatment: 4129757 INFO @ Sat, 08 Aug 2020 13:27:37: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 08 Aug 2020 13:27:37: #1 finished! INFO @ Sat, 08 Aug 2020 13:27:37: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:27:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:27:37: #2 number of paired peaks: 486 WARNING @ Sat, 08 Aug 2020 13:27:37: Fewer paired peaks (486) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 486 pairs to build model! INFO @ Sat, 08 Aug 2020 13:27:37: start model_add_line... INFO @ Sat, 08 Aug 2020 13:27:37: start X-correlation... INFO @ Sat, 08 Aug 2020 13:27:37: end of X-cor INFO @ Sat, 08 Aug 2020 13:27:37: #2 finished! INFO @ Sat, 08 Aug 2020 13:27:37: #2 predicted fragment length is 208 bps INFO @ Sat, 08 Aug 2020 13:27:37: #2 alternative fragment length(s) may be 208 bps INFO @ Sat, 08 Aug 2020 13:27:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8392422/SRX8392422.20_model.r WARNING @ Sat, 08 Aug 2020 13:27:37: #2 Since the d (208) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:27:37: #2 You may need to consider one of the other alternative d(s): 208 WARNING @ Sat, 08 Aug 2020 13:27:37: #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 13:27:37: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:27:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:27:47: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:27:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8392422/SRX8392422.20_peaks.xls INFO @ Sat, 08 Aug 2020 13:27:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8392422/SRX8392422.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:27:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8392422/SRX8392422.20_summits.bed INFO @ Sat, 08 Aug 2020 13:27:51: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (180 records, 4 fields): 1 millis CompletedMACS2peakCalling