Job ID = 16435252 SRX = SRX13336902 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: 01:02:25 24632080 reads; of these: 24632080 (100.00%) were paired; of these: 11732650 (47.63%) aligned concordantly 0 times 10960182 (44.50%) aligned concordantly exactly 1 time 1939248 (7.87%) aligned concordantly >1 times ---- 11732650 pairs aligned concordantly 0 times; of these: 5264155 (44.87%) aligned discordantly 1 time ---- 6468495 pairs aligned 0 times concordantly or discordantly; of these: 12936990 mates make up the pairs; of these: 10962464 (84.74%) aligned 0 times 923590 (7.14%) aligned exactly 1 time 1050936 (8.12%) aligned >1 times 77.75% overall alignment rate Time searching: 01:02:25 Overall time: 01:02:25 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] 1712290 / 18106606 = 0.0946 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 12:09:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13336902/SRX13336902.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13336902/SRX13336902.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13336902/SRX13336902.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13336902/SRX13336902.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 12:09:22: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:09:22: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:09:31: 1000000 INFO @ Tue, 02 Aug 2022 12:09:40: 2000000 INFO @ Tue, 02 Aug 2022 12:09:48: 3000000 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 12:09:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13336902/SRX13336902.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13336902/SRX13336902.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13336902/SRX13336902.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13336902/SRX13336902.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 12:09:51: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:09:51: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:10:00: 4000000 INFO @ Tue, 02 Aug 2022 12:10:04: 1000000 INFO @ Tue, 02 Aug 2022 12:10:10: 5000000 INFO @ Tue, 02 Aug 2022 12:10:18: 2000000 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 12:10:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13336902/SRX13336902.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13336902/SRX13336902.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13336902/SRX13336902.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13336902/SRX13336902.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 12:10:21: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:10:21: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:10:24: 6000000 INFO @ Tue, 02 Aug 2022 12:10:28: 3000000 INFO @ Tue, 02 Aug 2022 12:10:32: 1000000 INFO @ Tue, 02 Aug 2022 12:10:37: 7000000 INFO @ Tue, 02 Aug 2022 12:10:39: 4000000 INFO @ Tue, 02 Aug 2022 12:10:42: 2000000 INFO @ Tue, 02 Aug 2022 12:10:48: 8000000 INFO @ Tue, 02 Aug 2022 12:10:48: 5000000 INFO @ Tue, 02 Aug 2022 12:10:52: 3000000 INFO @ Tue, 02 Aug 2022 12:10:58: 6000000 INFO @ Tue, 02 Aug 2022 12:10:59: 9000000 INFO @ Tue, 02 Aug 2022 12:11:02: 4000000 INFO @ Tue, 02 Aug 2022 12:11:07: 7000000 INFO @ Tue, 02 Aug 2022 12:11:10: 10000000 INFO @ Tue, 02 Aug 2022 12:11:12: 5000000 INFO @ Tue, 02 Aug 2022 12:11:17: 8000000 INFO @ Tue, 02 Aug 2022 12:11:22: 11000000 INFO @ Tue, 02 Aug 2022 12:11:23: 6000000 INFO @ Tue, 02 Aug 2022 12:11:26: 9000000 INFO @ Tue, 02 Aug 2022 12:11:33: 7000000 INFO @ Tue, 02 Aug 2022 12:11:35: 10000000 INFO @ Tue, 02 Aug 2022 12:11:35: 12000000 INFO @ Tue, 02 Aug 2022 12:11:43: 8000000 INFO @ Tue, 02 Aug 2022 12:11:45: 11000000 INFO @ Tue, 02 Aug 2022 12:11:46: 13000000 INFO @ Tue, 02 Aug 2022 12:11:53: 9000000 INFO @ Tue, 02 Aug 2022 12:11:54: 12000000 INFO @ Tue, 02 Aug 2022 12:11:58: 14000000 INFO @ Tue, 02 Aug 2022 12:12:03: 10000000 INFO @ Tue, 02 Aug 2022 12:12:04: 13000000 INFO @ Tue, 02 Aug 2022 12:12:10: 15000000 INFO @ Tue, 02 Aug 2022 12:12:13: 14000000 INFO @ Tue, 02 Aug 2022 12:12:14: 11000000 INFO @ Tue, 02 Aug 2022 12:12:22: 15000000 INFO @ Tue, 02 Aug 2022 12:12:23: 16000000 INFO @ Tue, 02 Aug 2022 12:12:23: 12000000 INFO @ Tue, 02 Aug 2022 12:12:31: 16000000 INFO @ Tue, 02 Aug 2022 12:12:33: 13000000 INFO @ Tue, 02 Aug 2022 12:12:34: 17000000 INFO @ Tue, 02 Aug 2022 12:12:40: 17000000 INFO @ Tue, 02 Aug 2022 12:12:43: 14000000 INFO @ Tue, 02 Aug 2022 12:12:48: 18000000 INFO @ Tue, 02 Aug 2022 12:12:49: 18000000 INFO @ Tue, 02 Aug 2022 12:12:54: 15000000 INFO @ Tue, 02 Aug 2022 12:12:58: 19000000 INFO @ Tue, 02 Aug 2022 12:12:58: 19000000 INFO @ Tue, 02 Aug 2022 12:13:04: 16000000 INFO @ Tue, 02 Aug 2022 12:13:07: 20000000 INFO @ Tue, 02 Aug 2022 12:13:09: 20000000 INFO @ Tue, 02 Aug 2022 12:13:14: 17000000 INFO @ Tue, 02 Aug 2022 12:13:17: 21000000 INFO @ Tue, 02 Aug 2022 12:13:18: 21000000 INFO @ Tue, 02 Aug 2022 12:13:24: 18000000 INFO @ Tue, 02 Aug 2022 12:13:26: 22000000 INFO @ Tue, 02 Aug 2022 12:13:29: 22000000 INFO @ Tue, 02 Aug 2022 12:13:34: 19000000 INFO @ Tue, 02 Aug 2022 12:13:36: 23000000 INFO @ Tue, 02 Aug 2022 12:13:39: 23000000 INFO @ Tue, 02 Aug 2022 12:13:44: 20000000 INFO @ Tue, 02 Aug 2022 12:13:45: 24000000 INFO @ Tue, 02 Aug 2022 12:13:49: 24000000 INFO @ Tue, 02 Aug 2022 12:13:54: 21000000 INFO @ Tue, 02 Aug 2022 12:13:55: 25000000 INFO @ Tue, 02 Aug 2022 12:13:59: 25000000 INFO @ Tue, 02 Aug 2022 12:14:04: 22000000 INFO @ Tue, 02 Aug 2022 12:14:07: 26000000 INFO @ Tue, 02 Aug 2022 12:14:08: 26000000 INFO @ Tue, 02 Aug 2022 12:14:14: 23000000 INFO @ Tue, 02 Aug 2022 12:14:16: 27000000 INFO @ Tue, 02 Aug 2022 12:14:19: 27000000 INFO @ Tue, 02 Aug 2022 12:14:25: 24000000 INFO @ Tue, 02 Aug 2022 12:14:26: 28000000 INFO @ Tue, 02 Aug 2022 12:14:29: 28000000 INFO @ Tue, 02 Aug 2022 12:14:35: 29000000 INFO @ Tue, 02 Aug 2022 12:14:35: 25000000 INFO @ Tue, 02 Aug 2022 12:14:39: 29000000 INFO @ Tue, 02 Aug 2022 12:14:44: 30000000 INFO @ Tue, 02 Aug 2022 12:14:46: 26000000 INFO @ Tue, 02 Aug 2022 12:14:49: 30000000 INFO @ Tue, 02 Aug 2022 12:14:53: 31000000 INFO @ Tue, 02 Aug 2022 12:14:56: 27000000 INFO @ Tue, 02 Aug 2022 12:15:00: 31000000 INFO @ Tue, 02 Aug 2022 12:15:03: 32000000 INFO @ Tue, 02 Aug 2022 12:15:07: 28000000 INFO @ Tue, 02 Aug 2022 12:15:10: 32000000 INFO @ Tue, 02 Aug 2022 12:15:15: 33000000 INFO @ Tue, 02 Aug 2022 12:15:18: 29000000 INFO @ Tue, 02 Aug 2022 12:15:20: 33000000 INFO @ Tue, 02 Aug 2022 12:15:27: 34000000 INFO @ Tue, 02 Aug 2022 12:15:30: 30000000 INFO @ Tue, 02 Aug 2022 12:15:31: 34000000 INFO @ Tue, 02 Aug 2022 12:15:36: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 12:15:36: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 12:15:36: #1 total tags in treatment: 11570254 INFO @ Tue, 02 Aug 2022 12:15:36: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:15:36: #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 12:15:36: #1 tags after filtering in treatment: 10509204 INFO @ Tue, 02 Aug 2022 12:15:36: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 02 Aug 2022 12:15:36: #1 finished! INFO @ Tue, 02 Aug 2022 12:15:36: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:15:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:15:37: #2 number of paired peaks: 480 WARNING @ Tue, 02 Aug 2022 12:15:37: Fewer paired peaks (480) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 480 pairs to build model! INFO @ Tue, 02 Aug 2022 12:15:37: start model_add_line... INFO @ Tue, 02 Aug 2022 12:15:37: start X-correlation... INFO @ Tue, 02 Aug 2022 12:15:37: end of X-cor INFO @ Tue, 02 Aug 2022 12:15:37: #2 finished! INFO @ Tue, 02 Aug 2022 12:15:37: #2 predicted fragment length is 224 bps INFO @ Tue, 02 Aug 2022 12:15:37: #2 alternative fragment length(s) may be 224 bps INFO @ Tue, 02 Aug 2022 12:15:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13336902/SRX13336902.10_model.r WARNING @ Tue, 02 Aug 2022 12:15:37: #2 Since the d (224) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 12:15:37: #2 You may need to consider one of the other alternative d(s): 224 WARNING @ Tue, 02 Aug 2022 12:15:37: #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 12:15:37: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:15:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:15:41: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 12:15:41: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 12:15:41: #1 total tags in treatment: 11570254 INFO @ Tue, 02 Aug 2022 12:15:41: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:15:41: #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 12:15:41: #1 tags after filtering in treatment: 10509204 INFO @ Tue, 02 Aug 2022 12:15:41: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 02 Aug 2022 12:15:41: #1 finished! INFO @ Tue, 02 Aug 2022 12:15:41: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:15:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:15:42: 31000000 INFO @ Tue, 02 Aug 2022 12:15:42: #2 number of paired peaks: 480 WARNING @ Tue, 02 Aug 2022 12:15:42: Fewer paired peaks (480) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 480 pairs to build model! INFO @ Tue, 02 Aug 2022 12:15:42: start model_add_line... INFO @ Tue, 02 Aug 2022 12:15:42: start X-correlation... INFO @ Tue, 02 Aug 2022 12:15:42: end of X-cor INFO @ Tue, 02 Aug 2022 12:15:42: #2 finished! INFO @ Tue, 02 Aug 2022 12:15:42: #2 predicted fragment length is 224 bps INFO @ Tue, 02 Aug 2022 12:15:42: #2 alternative fragment length(s) may be 224 bps INFO @ Tue, 02 Aug 2022 12:15:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13336902/SRX13336902.05_model.r WARNING @ Tue, 02 Aug 2022 12:15:42: #2 Since the d (224) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 12:15:42: #2 You may need to consider one of the other alternative d(s): 224 WARNING @ Tue, 02 Aug 2022 12:15:42: #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 12:15:42: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:15:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:15:53: 32000000 INFO @ Tue, 02 Aug 2022 12:16:00: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 12:16:04: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:16:05: 33000000 INFO @ Tue, 02 Aug 2022 12:16:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13336902/SRX13336902.10_peaks.xls INFO @ Tue, 02 Aug 2022 12:16:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13336902/SRX13336902.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:16:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13336902/SRX13336902.10_summits.bed INFO @ Tue, 02 Aug 2022 12:16:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (384 records, 4 fields): 85 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 12:16:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13336902/SRX13336902.05_peaks.xls INFO @ Tue, 02 Aug 2022 12:16:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13336902/SRX13336902.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:16:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13336902/SRX13336902.05_summits.bed INFO @ Tue, 02 Aug 2022 12:16:14: Done! pass1 - making usageList (7 chroms): 13 millis pass2 - checking and writing primary data (488 records, 4 fields): 72 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 12:16:17: 34000000 INFO @ Tue, 02 Aug 2022 12:16:27: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 12:16:27: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 12:16:27: #1 total tags in treatment: 11570254 INFO @ Tue, 02 Aug 2022 12:16:27: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:16:27: #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 12:16:27: #1 tags after filtering in treatment: 10509204 INFO @ Tue, 02 Aug 2022 12:16:27: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 02 Aug 2022 12:16:27: #1 finished! INFO @ Tue, 02 Aug 2022 12:16:27: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:16:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:16:28: #2 number of paired peaks: 480 WARNING @ Tue, 02 Aug 2022 12:16:28: Fewer paired peaks (480) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 480 pairs to build model! INFO @ Tue, 02 Aug 2022 12:16:28: start model_add_line... INFO @ Tue, 02 Aug 2022 12:16:28: start X-correlation... INFO @ Tue, 02 Aug 2022 12:16:28: end of X-cor INFO @ Tue, 02 Aug 2022 12:16:28: #2 finished! INFO @ Tue, 02 Aug 2022 12:16:28: #2 predicted fragment length is 224 bps INFO @ Tue, 02 Aug 2022 12:16:28: #2 alternative fragment length(s) may be 224 bps INFO @ Tue, 02 Aug 2022 12:16:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13336902/SRX13336902.20_model.r WARNING @ Tue, 02 Aug 2022 12:16:28: #2 Since the d (224) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 12:16:28: #2 You may need to consider one of the other alternative d(s): 224 WARNING @ Tue, 02 Aug 2022 12:16:28: #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 12:16:28: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:16:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:16:51: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:17:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13336902/SRX13336902.20_peaks.xls INFO @ Tue, 02 Aug 2022 12:17:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13336902/SRX13336902.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:17:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13336902/SRX13336902.20_summits.bed INFO @ Tue, 02 Aug 2022 12:17:01: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (280 records, 4 fields): 21 millis CompletedMACS2peakCalling BigWig に変換しました。