Job ID = 12265428 SRX = SRX7246270 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: 00:27:07 19727431 reads; of these: 19727431 (100.00%) were paired; of these: 922866 (4.68%) aligned concordantly 0 times 15328077 (77.70%) aligned concordantly exactly 1 time 3476488 (17.62%) aligned concordantly >1 times ---- 922866 pairs aligned concordantly 0 times; of these: 250509 (27.14%) aligned discordantly 1 time ---- 672357 pairs aligned 0 times concordantly or discordantly; of these: 1344714 mates make up the pairs; of these: 918734 (68.32%) aligned 0 times 264393 (19.66%) aligned exactly 1 time 161587 (12.02%) aligned >1 times 97.67% overall alignment rate Time searching: 00:27:07 Overall time: 00:27:07 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 16 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] 3037325 / 12485348 = 0.2433 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:42:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7246270/SRX7246270.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7246270/SRX7246270.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7246270/SRX7246270.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7246270/SRX7246270.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, 03 Apr 2021 07:42:12: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:42:12: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:42:18: 1000000 INFO @ Sat, 03 Apr 2021 07:42:24: 2000000 INFO @ Sat, 03 Apr 2021 07:42:30: 3000000 INFO @ Sat, 03 Apr 2021 07:42:36: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:42:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7246270/SRX7246270.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7246270/SRX7246270.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7246270/SRX7246270.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7246270/SRX7246270.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, 03 Apr 2021 07:42:41: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:42:41: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:42:43: 5000000 INFO @ Sat, 03 Apr 2021 07:42:48: 1000000 INFO @ Sat, 03 Apr 2021 07:42:49: 6000000 INFO @ Sat, 03 Apr 2021 07:42:54: 2000000 INFO @ Sat, 03 Apr 2021 07:42:56: 7000000 INFO @ Sat, 03 Apr 2021 07:43:01: 3000000 INFO @ Sat, 03 Apr 2021 07:43:02: 8000000 INFO @ Sat, 03 Apr 2021 07:43:07: 4000000 INFO @ Sat, 03 Apr 2021 07:43:09: 9000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:43:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7246270/SRX7246270.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7246270/SRX7246270.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7246270/SRX7246270.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7246270/SRX7246270.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, 03 Apr 2021 07:43:11: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:43:11: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:43:14: 5000000 INFO @ Sat, 03 Apr 2021 07:43:15: 10000000 INFO @ Sat, 03 Apr 2021 07:43:18: 1000000 INFO @ Sat, 03 Apr 2021 07:43:20: 6000000 INFO @ Sat, 03 Apr 2021 07:43:22: 11000000 INFO @ Sat, 03 Apr 2021 07:43:24: 2000000 INFO @ Sat, 03 Apr 2021 07:43:27: 7000000 INFO @ Sat, 03 Apr 2021 07:43:29: 12000000 INFO @ Sat, 03 Apr 2021 07:43:31: 3000000 INFO @ Sat, 03 Apr 2021 07:43:33: 8000000 INFO @ Sat, 03 Apr 2021 07:43:36: 13000000 INFO @ Sat, 03 Apr 2021 07:43:38: 4000000 INFO @ Sat, 03 Apr 2021 07:43:40: 9000000 INFO @ Sat, 03 Apr 2021 07:43:42: 14000000 INFO @ Sat, 03 Apr 2021 07:43:44: 5000000 INFO @ Sat, 03 Apr 2021 07:43:46: 10000000 INFO @ Sat, 03 Apr 2021 07:43:49: 15000000 INFO @ Sat, 03 Apr 2021 07:43:51: 6000000 INFO @ Sat, 03 Apr 2021 07:43:53: 11000000 INFO @ Sat, 03 Apr 2021 07:43:56: 16000000 INFO @ Sat, 03 Apr 2021 07:43:57: 7000000 INFO @ Sat, 03 Apr 2021 07:44:00: 12000000 INFO @ Sat, 03 Apr 2021 07:44:02: 17000000 INFO @ Sat, 03 Apr 2021 07:44:04: 8000000 INFO @ Sat, 03 Apr 2021 07:44:06: 13000000 INFO @ Sat, 03 Apr 2021 07:44:09: 18000000 INFO @ Sat, 03 Apr 2021 07:44:11: 9000000 INFO @ Sat, 03 Apr 2021 07:44:13: 14000000 INFO @ Sat, 03 Apr 2021 07:44:16: 19000000 INFO @ Sat, 03 Apr 2021 07:44:17: 10000000 INFO @ Sat, 03 Apr 2021 07:44:19: 15000000 INFO @ Sat, 03 Apr 2021 07:44:23: 20000000 INFO @ Sat, 03 Apr 2021 07:44:24: 11000000 INFO @ Sat, 03 Apr 2021 07:44:26: 16000000 INFO @ Sat, 03 Apr 2021 07:44:29: 21000000 INFO @ Sat, 03 Apr 2021 07:44:30: 12000000 INFO @ Sat, 03 Apr 2021 07:44:33: 17000000 INFO @ Sat, 03 Apr 2021 07:44:36: 22000000 INFO @ Sat, 03 Apr 2021 07:44:37: 13000000 INFO @ Sat, 03 Apr 2021 07:44:39: 18000000 INFO @ Sat, 03 Apr 2021 07:44:43: 23000000 INFO @ Sat, 03 Apr 2021 07:44:44: 14000000 INFO @ Sat, 03 Apr 2021 07:44:46: 19000000 INFO @ Sat, 03 Apr 2021 07:44:49: 24000000 INFO @ Sat, 03 Apr 2021 07:44:50: 15000000 INFO @ Sat, 03 Apr 2021 07:44:53: 20000000 INFO @ Sat, 03 Apr 2021 07:44:56: 25000000 INFO @ Sat, 03 Apr 2021 07:44:57: 16000000 INFO @ Sat, 03 Apr 2021 07:44:59: 21000000 INFO @ Sat, 03 Apr 2021 07:45:03: 26000000 INFO @ Sat, 03 Apr 2021 07:45:04: 17000000 INFO @ Sat, 03 Apr 2021 07:45:06: 22000000 INFO @ Sat, 03 Apr 2021 07:45:09: 27000000 INFO @ Sat, 03 Apr 2021 07:45:10: 18000000 INFO @ Sat, 03 Apr 2021 07:45:12: 23000000 INFO @ Sat, 03 Apr 2021 07:45:16: 28000000 INFO @ Sat, 03 Apr 2021 07:45:17: 19000000 INFO @ Sat, 03 Apr 2021 07:45:19: 24000000 INFO @ Sat, 03 Apr 2021 07:45:23: 29000000 INFO @ Sat, 03 Apr 2021 07:45:24: 20000000 INFO @ Sat, 03 Apr 2021 07:45:26: 25000000 INFO @ Sat, 03 Apr 2021 07:45:30: 30000000 INFO @ Sat, 03 Apr 2021 07:45:31: 21000000 INFO @ Sat, 03 Apr 2021 07:45:32: 26000000 INFO @ Sat, 03 Apr 2021 07:45:36: 31000000 INFO @ Sat, 03 Apr 2021 07:45:37: 22000000 INFO @ Sat, 03 Apr 2021 07:45:39: 27000000 INFO @ Sat, 03 Apr 2021 07:45:43: 32000000 INFO @ Sat, 03 Apr 2021 07:45:44: 23000000 INFO @ Sat, 03 Apr 2021 07:45:46: 28000000 INFO @ Sat, 03 Apr 2021 07:45:46: #1 tag size is determined as 92 bps INFO @ Sat, 03 Apr 2021 07:45:46: #1 tag size = 92 INFO @ Sat, 03 Apr 2021 07:45:46: #1 total tags in treatment: 15772039 INFO @ Sat, 03 Apr 2021 07:45:46: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:45:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:45:46: #1 tags after filtering in treatment: 10717121 INFO @ Sat, 03 Apr 2021 07:45:46: #1 Redundant rate of treatment: 0.32 INFO @ Sat, 03 Apr 2021 07:45:46: #1 finished! INFO @ Sat, 03 Apr 2021 07:45:46: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:45:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:45:47: #2 number of paired peaks: 306 WARNING @ Sat, 03 Apr 2021 07:45:47: Fewer paired peaks (306) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 306 pairs to build model! INFO @ Sat, 03 Apr 2021 07:45:47: start model_add_line... INFO @ Sat, 03 Apr 2021 07:45:47: start X-correlation... INFO @ Sat, 03 Apr 2021 07:45:47: end of X-cor INFO @ Sat, 03 Apr 2021 07:45:47: #2 finished! INFO @ Sat, 03 Apr 2021 07:45:47: #2 predicted fragment length is 98 bps INFO @ Sat, 03 Apr 2021 07:45:47: #2 alternative fragment length(s) may be 98 bps INFO @ Sat, 03 Apr 2021 07:45:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7246270/SRX7246270.05_model.r WARNING @ Sat, 03 Apr 2021 07:45:47: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:45:47: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Sat, 03 Apr 2021 07:45:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:45:47: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:45:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:45:50: 24000000 INFO @ Sat, 03 Apr 2021 07:45:52: 29000000 INFO @ Sat, 03 Apr 2021 07:45:57: 25000000 INFO @ Sat, 03 Apr 2021 07:45:59: 30000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:46:04: 26000000 INFO @ Sat, 03 Apr 2021 07:46:05: 31000000 INFO @ Sat, 03 Apr 2021 07:46:10: 27000000 INFO @ Sat, 03 Apr 2021 07:46:12: 32000000 INFO @ Sat, 03 Apr 2021 07:46:13: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:46:15: #1 tag size is determined as 92 bps INFO @ Sat, 03 Apr 2021 07:46:15: #1 tag size = 92 INFO @ Sat, 03 Apr 2021 07:46:15: #1 total tags in treatment: 15772039 INFO @ Sat, 03 Apr 2021 07:46:15: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:46:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:46:15: #1 tags after filtering in treatment: 10717121 INFO @ Sat, 03 Apr 2021 07:46:15: #1 Redundant rate of treatment: 0.32 INFO @ Sat, 03 Apr 2021 07:46:15: #1 finished! INFO @ Sat, 03 Apr 2021 07:46:15: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:46:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:46:16: #2 number of paired peaks: 306 WARNING @ Sat, 03 Apr 2021 07:46:16: Fewer paired peaks (306) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 306 pairs to build model! INFO @ Sat, 03 Apr 2021 07:46:16: start model_add_line... INFO @ Sat, 03 Apr 2021 07:46:16: start X-correlation... INFO @ Sat, 03 Apr 2021 07:46:16: end of X-cor INFO @ Sat, 03 Apr 2021 07:46:16: #2 finished! INFO @ Sat, 03 Apr 2021 07:46:16: #2 predicted fragment length is 98 bps INFO @ Sat, 03 Apr 2021 07:46:16: #2 alternative fragment length(s) may be 98 bps INFO @ Sat, 03 Apr 2021 07:46:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7246270/SRX7246270.10_model.r WARNING @ Sat, 03 Apr 2021 07:46:16: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:46:16: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Sat, 03 Apr 2021 07:46:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:46:16: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:46:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:46:17: 28000000 INFO @ Sat, 03 Apr 2021 07:46:23: 29000000 INFO @ Sat, 03 Apr 2021 07:46:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7246270/SRX7246270.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:46:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7246270/SRX7246270.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:46:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7246270/SRX7246270.05_summits.bed INFO @ Sat, 03 Apr 2021 07:46:26: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3788 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:46:29: 30000000 INFO @ Sat, 03 Apr 2021 07:46:36: 31000000 INFO @ Sat, 03 Apr 2021 07:46:40: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:46:42: 32000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:46:45: #1 tag size is determined as 92 bps INFO @ Sat, 03 Apr 2021 07:46:45: #1 tag size = 92 INFO @ Sat, 03 Apr 2021 07:46:45: #1 total tags in treatment: 15772039 INFO @ Sat, 03 Apr 2021 07:46:45: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:46:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:46:45: #1 tags after filtering in treatment: 10717121 INFO @ Sat, 03 Apr 2021 07:46:45: #1 Redundant rate of treatment: 0.32 INFO @ Sat, 03 Apr 2021 07:46:45: #1 finished! INFO @ Sat, 03 Apr 2021 07:46:45: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:46:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:46:46: #2 number of paired peaks: 306 WARNING @ Sat, 03 Apr 2021 07:46:46: Fewer paired peaks (306) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 306 pairs to build model! INFO @ Sat, 03 Apr 2021 07:46:46: start model_add_line... INFO @ Sat, 03 Apr 2021 07:46:46: start X-correlation... INFO @ Sat, 03 Apr 2021 07:46:46: end of X-cor INFO @ Sat, 03 Apr 2021 07:46:46: #2 finished! INFO @ Sat, 03 Apr 2021 07:46:46: #2 predicted fragment length is 98 bps INFO @ Sat, 03 Apr 2021 07:46:46: #2 alternative fragment length(s) may be 98 bps INFO @ Sat, 03 Apr 2021 07:46:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7246270/SRX7246270.20_model.r WARNING @ Sat, 03 Apr 2021 07:46:46: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:46:46: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Sat, 03 Apr 2021 07:46:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:46:46: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:46:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:46:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7246270/SRX7246270.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:46:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7246270/SRX7246270.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:46:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7246270/SRX7246270.10_summits.bed INFO @ Sat, 03 Apr 2021 07:46:52: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2112 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:47:10: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:47:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7246270/SRX7246270.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:47:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7246270/SRX7246270.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:47:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7246270/SRX7246270.20_summits.bed INFO @ Sat, 03 Apr 2021 07:47:22: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (873 records, 4 fields): 3 millis CompletedMACS2peakCalling