Job ID = 16435019 SRX = SRX13336912 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: 00:38:27 21758942 reads; of these: 21758942 (100.00%) were paired; of these: 9116606 (41.90%) aligned concordantly 0 times 10798419 (49.63%) aligned concordantly exactly 1 time 1843917 (8.47%) aligned concordantly >1 times ---- 9116606 pairs aligned concordantly 0 times; of these: 3663329 (40.18%) aligned discordantly 1 time ---- 5453277 pairs aligned 0 times concordantly or discordantly; of these: 10906554 mates make up the pairs; of these: 9611085 (88.12%) aligned 0 times 577464 (5.29%) aligned exactly 1 time 718005 (6.58%) aligned >1 times 77.91% overall alignment rate Time searching: 00:38:27 Overall time: 00:38:27 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 28 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] 1446909 / 16234483 = 0.0891 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 11:26:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13336912/SRX13336912.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13336912/SRX13336912.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13336912/SRX13336912.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13336912/SRX13336912.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 @ Tue, 02 Aug 2022 11:26:33: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:26:33: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:26:39: 1000000 INFO @ Tue, 02 Aug 2022 11:26:45: 2000000 INFO @ Tue, 02 Aug 2022 11:26:51: 3000000 INFO @ Tue, 02 Aug 2022 11:26:57: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 11:27:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13336912/SRX13336912.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13336912/SRX13336912.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13336912/SRX13336912.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13336912/SRX13336912.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 @ Tue, 02 Aug 2022 11:27:01: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:27:01: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:27:04: 5000000 INFO @ Tue, 02 Aug 2022 11:27:08: 1000000 INFO @ Tue, 02 Aug 2022 11:27:10: 6000000 INFO @ Tue, 02 Aug 2022 11:27:14: 2000000 INFO @ Tue, 02 Aug 2022 11:27:16: 7000000 INFO @ Tue, 02 Aug 2022 11:27:21: 3000000 INFO @ Tue, 02 Aug 2022 11:27:23: 8000000 INFO @ Tue, 02 Aug 2022 11:27:27: 4000000 INFO @ Tue, 02 Aug 2022 11:27:29: 9000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 11:27:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13336912/SRX13336912.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13336912/SRX13336912.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13336912/SRX13336912.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13336912/SRX13336912.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 @ Tue, 02 Aug 2022 11:27:31: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:27:31: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:27:33: 5000000 INFO @ Tue, 02 Aug 2022 11:27:35: 10000000 INFO @ Tue, 02 Aug 2022 11:27:38: 1000000 INFO @ Tue, 02 Aug 2022 11:27:40: 6000000 INFO @ Tue, 02 Aug 2022 11:27:42: 11000000 INFO @ Tue, 02 Aug 2022 11:27:44: 2000000 INFO @ Tue, 02 Aug 2022 11:27:46: 7000000 INFO @ Tue, 02 Aug 2022 11:27:48: 12000000 INFO @ Tue, 02 Aug 2022 11:27:51: 3000000 INFO @ Tue, 02 Aug 2022 11:27:53: 8000000 INFO @ Tue, 02 Aug 2022 11:27:54: 13000000 INFO @ Tue, 02 Aug 2022 11:27:57: 4000000 INFO @ Tue, 02 Aug 2022 11:27:59: 9000000 INFO @ Tue, 02 Aug 2022 11:28:01: 14000000 INFO @ Tue, 02 Aug 2022 11:28:03: 5000000 INFO @ Tue, 02 Aug 2022 11:28:05: 10000000 INFO @ Tue, 02 Aug 2022 11:28:07: 15000000 INFO @ Tue, 02 Aug 2022 11:28:10: 6000000 INFO @ Tue, 02 Aug 2022 11:28:12: 11000000 INFO @ Tue, 02 Aug 2022 11:28:13: 16000000 INFO @ Tue, 02 Aug 2022 11:28:16: 7000000 INFO @ Tue, 02 Aug 2022 11:28:18: 12000000 INFO @ Tue, 02 Aug 2022 11:28:20: 17000000 INFO @ Tue, 02 Aug 2022 11:28:23: 8000000 INFO @ Tue, 02 Aug 2022 11:28:24: 13000000 INFO @ Tue, 02 Aug 2022 11:28:26: 18000000 INFO @ Tue, 02 Aug 2022 11:28:29: 9000000 INFO @ Tue, 02 Aug 2022 11:28:31: 14000000 INFO @ Tue, 02 Aug 2022 11:28:32: 19000000 INFO @ Tue, 02 Aug 2022 11:28:35: 10000000 INFO @ Tue, 02 Aug 2022 11:28:37: 15000000 INFO @ Tue, 02 Aug 2022 11:28:39: 20000000 INFO @ Tue, 02 Aug 2022 11:28:42: 11000000 INFO @ Tue, 02 Aug 2022 11:28:44: 16000000 INFO @ Tue, 02 Aug 2022 11:28:45: 21000000 INFO @ Tue, 02 Aug 2022 11:28:48: 12000000 INFO @ Tue, 02 Aug 2022 11:28:50: 17000000 INFO @ Tue, 02 Aug 2022 11:28:51: 22000000 INFO @ Tue, 02 Aug 2022 11:28:55: 13000000 INFO @ Tue, 02 Aug 2022 11:28:56: 18000000 INFO @ Tue, 02 Aug 2022 11:28:58: 23000000 INFO @ Tue, 02 Aug 2022 11:29:01: 14000000 INFO @ Tue, 02 Aug 2022 11:29:03: 19000000 INFO @ Tue, 02 Aug 2022 11:29:04: 24000000 INFO @ Tue, 02 Aug 2022 11:29:07: 15000000 INFO @ Tue, 02 Aug 2022 11:29:09: 20000000 INFO @ Tue, 02 Aug 2022 11:29:10: 25000000 INFO @ Tue, 02 Aug 2022 11:29:14: 16000000 INFO @ Tue, 02 Aug 2022 11:29:16: 21000000 INFO @ Tue, 02 Aug 2022 11:29:17: 26000000 INFO @ Tue, 02 Aug 2022 11:29:21: 17000000 INFO @ Tue, 02 Aug 2022 11:29:22: 22000000 INFO @ Tue, 02 Aug 2022 11:29:24: 27000000 INFO @ Tue, 02 Aug 2022 11:29:27: 18000000 INFO @ Tue, 02 Aug 2022 11:29:29: 23000000 INFO @ Tue, 02 Aug 2022 11:29:30: 28000000 INFO @ Tue, 02 Aug 2022 11:29:34: 19000000 INFO @ Tue, 02 Aug 2022 11:29:35: 24000000 INFO @ Tue, 02 Aug 2022 11:29:37: 29000000 INFO @ Tue, 02 Aug 2022 11:29:41: 20000000 INFO @ Tue, 02 Aug 2022 11:29:42: 25000000 INFO @ Tue, 02 Aug 2022 11:29:44: 30000000 INFO @ Tue, 02 Aug 2022 11:29:47: 21000000 INFO @ Tue, 02 Aug 2022 11:29:48: 26000000 INFO @ Tue, 02 Aug 2022 11:29:51: 31000000 INFO @ Tue, 02 Aug 2022 11:29:51: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 11:29:51: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 11:29:51: #1 total tags in treatment: 11451580 INFO @ Tue, 02 Aug 2022 11:29:51: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:29:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 11:29:51: #1 tags after filtering in treatment: 10554875 INFO @ Tue, 02 Aug 2022 11:29:51: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 02 Aug 2022 11:29:51: #1 finished! INFO @ Tue, 02 Aug 2022 11:29:51: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:29:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:29:52: #2 number of paired peaks: 440 WARNING @ Tue, 02 Aug 2022 11:29:52: Fewer paired peaks (440) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 440 pairs to build model! INFO @ Tue, 02 Aug 2022 11:29:52: start model_add_line... INFO @ Tue, 02 Aug 2022 11:29:52: start X-correlation... INFO @ Tue, 02 Aug 2022 11:29:52: end of X-cor INFO @ Tue, 02 Aug 2022 11:29:52: #2 finished! INFO @ Tue, 02 Aug 2022 11:29:52: #2 predicted fragment length is 216 bps INFO @ Tue, 02 Aug 2022 11:29:52: #2 alternative fragment length(s) may be 216 bps INFO @ Tue, 02 Aug 2022 11:29:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13336912/SRX13336912.05_model.r WARNING @ Tue, 02 Aug 2022 11:29:52: #2 Since the d (216) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:29:52: #2 You may need to consider one of the other alternative d(s): 216 WARNING @ Tue, 02 Aug 2022 11:29:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 11:29:52: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:29:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:29:54: 22000000 INFO @ Tue, 02 Aug 2022 11:29:54: 27000000 INFO @ Tue, 02 Aug 2022 11:30:00: 23000000 INFO @ Tue, 02 Aug 2022 11:30:00: 28000000 INFO @ Tue, 02 Aug 2022 11:30:06: 24000000 INFO @ Tue, 02 Aug 2022 11:30:07: 29000000 INFO @ Tue, 02 Aug 2022 11:30:12: 25000000 INFO @ Tue, 02 Aug 2022 11:30:13: 30000000 INFO @ Tue, 02 Aug 2022 11:30:15: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 11:30:18: 26000000 INFO @ Tue, 02 Aug 2022 11:30:19: 31000000 INFO @ Tue, 02 Aug 2022 11:30:19: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 11:30:19: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 11:30:19: #1 total tags in treatment: 11451580 INFO @ Tue, 02 Aug 2022 11:30:19: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:30:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 11:30:20: #1 tags after filtering in treatment: 10554875 INFO @ Tue, 02 Aug 2022 11:30:20: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 02 Aug 2022 11:30:20: #1 finished! INFO @ Tue, 02 Aug 2022 11:30:20: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:30:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:30:20: #2 number of paired peaks: 440 WARNING @ Tue, 02 Aug 2022 11:30:20: Fewer paired peaks (440) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 440 pairs to build model! INFO @ Tue, 02 Aug 2022 11:30:20: start model_add_line... INFO @ Tue, 02 Aug 2022 11:30:20: start X-correlation... INFO @ Tue, 02 Aug 2022 11:30:20: end of X-cor INFO @ Tue, 02 Aug 2022 11:30:20: #2 finished! INFO @ Tue, 02 Aug 2022 11:30:20: #2 predicted fragment length is 216 bps INFO @ Tue, 02 Aug 2022 11:30:20: #2 alternative fragment length(s) may be 216 bps INFO @ Tue, 02 Aug 2022 11:30:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13336912/SRX13336912.10_model.r WARNING @ Tue, 02 Aug 2022 11:30:21: #2 Since the d (216) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:30:21: #2 You may need to consider one of the other alternative d(s): 216 WARNING @ Tue, 02 Aug 2022 11:30:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 11:30:21: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:30:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:30:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13336912/SRX13336912.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:30:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13336912/SRX13336912.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:30:25: 27000000 INFO @ Tue, 02 Aug 2022 11:30:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13336912/SRX13336912.05_summits.bed INFO @ Tue, 02 Aug 2022 11:30:25: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (467 records, 4 fields): 39 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:30:31: 28000000 INFO @ Tue, 02 Aug 2022 11:30:37: 29000000 INFO @ Tue, 02 Aug 2022 11:30:43: 30000000 INFO @ Tue, 02 Aug 2022 11:30:43: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:30:49: 31000000 INFO @ Tue, 02 Aug 2022 11:30:49: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 11:30:49: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 11:30:49: #1 total tags in treatment: 11451580 INFO @ Tue, 02 Aug 2022 11:30:49: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:30:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 11:30:49: #1 tags after filtering in treatment: 10554875 INFO @ Tue, 02 Aug 2022 11:30:49: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 02 Aug 2022 11:30:49: #1 finished! INFO @ Tue, 02 Aug 2022 11:30:49: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:30:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:30:50: #2 number of paired peaks: 440 WARNING @ Tue, 02 Aug 2022 11:30:50: Fewer paired peaks (440) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 440 pairs to build model! INFO @ Tue, 02 Aug 2022 11:30:50: start model_add_line... INFO @ Tue, 02 Aug 2022 11:30:50: start X-correlation... INFO @ Tue, 02 Aug 2022 11:30:50: end of X-cor INFO @ Tue, 02 Aug 2022 11:30:50: #2 finished! INFO @ Tue, 02 Aug 2022 11:30:50: #2 predicted fragment length is 216 bps INFO @ Tue, 02 Aug 2022 11:30:50: #2 alternative fragment length(s) may be 216 bps INFO @ Tue, 02 Aug 2022 11:30:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13336912/SRX13336912.20_model.r WARNING @ Tue, 02 Aug 2022 11:30:50: #2 Since the d (216) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:30:50: #2 You may need to consider one of the other alternative d(s): 216 WARNING @ Tue, 02 Aug 2022 11:30:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 11:30:50: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:30:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:30:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13336912/SRX13336912.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:30:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13336912/SRX13336912.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:30:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13336912/SRX13336912.10_summits.bed INFO @ Tue, 02 Aug 2022 11:30:53: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (362 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:31:13: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 11:31:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13336912/SRX13336912.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:31:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13336912/SRX13336912.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:31:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13336912/SRX13336912.20_summits.bed INFO @ Tue, 02 Aug 2022 11:31:23: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (263 records, 4 fields): 21 millis CompletedMACS2peakCalling