Job ID = 16435014 SRX = SRX13336910 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:50:25 24406548 reads; of these: 24406548 (100.00%) were paired; of these: 13385313 (54.84%) aligned concordantly 0 times 9933677 (40.70%) aligned concordantly exactly 1 time 1087558 (4.46%) aligned concordantly >1 times ---- 13385313 pairs aligned concordantly 0 times; of these: 5592828 (41.78%) aligned discordantly 1 time ---- 7792485 pairs aligned 0 times concordantly or discordantly; of these: 15584970 mates make up the pairs; of these: 13590394 (87.20%) aligned 0 times 1067399 (6.85%) aligned exactly 1 time 927177 (5.95%) aligned >1 times 72.16% overall alignment rate Time searching: 00:50:26 Overall time: 00:50:26 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] 1524502 / 16580678 = 0.0919 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 11:52:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13336910/SRX13336910.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13336910/SRX13336910.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13336910/SRX13336910.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13336910/SRX13336910.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 11:52:13: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:52:13: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:52:23: 1000000 INFO @ Tue, 02 Aug 2022 11:52:33: 2000000 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 11:52:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13336910/SRX13336910.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13336910/SRX13336910.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13336910/SRX13336910.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13336910/SRX13336910.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 11:52:41: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:52:41: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:52:43: 3000000 INFO @ Tue, 02 Aug 2022 11:52:50: 1000000 INFO @ Tue, 02 Aug 2022 11:52:53: 4000000 INFO @ Tue, 02 Aug 2022 11:52:58: 2000000 INFO @ Tue, 02 Aug 2022 11:53:03: 5000000 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 11:53:09: 3000000 INFO @ Tue, 02 Aug 2022 11:53:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13336910/SRX13336910.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13336910/SRX13336910.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13336910/SRX13336910.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13336910/SRX13336910.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 11:53:11: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:53:11: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:53:14: 6000000 INFO @ Tue, 02 Aug 2022 11:53:21: 4000000 INFO @ Tue, 02 Aug 2022 11:53:23: 1000000 INFO @ Tue, 02 Aug 2022 11:53:26: 7000000 INFO @ Tue, 02 Aug 2022 11:53:33: 5000000 INFO @ Tue, 02 Aug 2022 11:53:35: 2000000 INFO @ Tue, 02 Aug 2022 11:53:40: 8000000 INFO @ Tue, 02 Aug 2022 11:53:45: 3000000 INFO @ Tue, 02 Aug 2022 11:53:46: 6000000 INFO @ Tue, 02 Aug 2022 11:53:52: 9000000 INFO @ Tue, 02 Aug 2022 11:53:55: 4000000 INFO @ Tue, 02 Aug 2022 11:53:59: 7000000 INFO @ Tue, 02 Aug 2022 11:54:06: 10000000 INFO @ Tue, 02 Aug 2022 11:54:08: 5000000 INFO @ Tue, 02 Aug 2022 11:54:11: 8000000 INFO @ Tue, 02 Aug 2022 11:54:18: 11000000 INFO @ Tue, 02 Aug 2022 11:54:20: 6000000 INFO @ Tue, 02 Aug 2022 11:54:23: 9000000 INFO @ Tue, 02 Aug 2022 11:54:30: 7000000 INFO @ Tue, 02 Aug 2022 11:54:31: 12000000 INFO @ Tue, 02 Aug 2022 11:54:34: 10000000 INFO @ Tue, 02 Aug 2022 11:54:40: 8000000 INFO @ Tue, 02 Aug 2022 11:54:45: 13000000 INFO @ Tue, 02 Aug 2022 11:54:46: 11000000 INFO @ Tue, 02 Aug 2022 11:54:50: 9000000 INFO @ Tue, 02 Aug 2022 11:54:58: 12000000 INFO @ Tue, 02 Aug 2022 11:54:59: 14000000 INFO @ Tue, 02 Aug 2022 11:55:01: 10000000 INFO @ Tue, 02 Aug 2022 11:55:11: 11000000 INFO @ Tue, 02 Aug 2022 11:55:11: 13000000 INFO @ Tue, 02 Aug 2022 11:55:14: 15000000 INFO @ Tue, 02 Aug 2022 11:55:21: 12000000 INFO @ Tue, 02 Aug 2022 11:55:23: 14000000 INFO @ Tue, 02 Aug 2022 11:55:26: 16000000 INFO @ Tue, 02 Aug 2022 11:55:31: 13000000 INFO @ Tue, 02 Aug 2022 11:55:35: 15000000 INFO @ Tue, 02 Aug 2022 11:55:38: 17000000 INFO @ Tue, 02 Aug 2022 11:55:40: 14000000 INFO @ Tue, 02 Aug 2022 11:55:47: 16000000 INFO @ Tue, 02 Aug 2022 11:55:50: 18000000 INFO @ Tue, 02 Aug 2022 11:55:51: 15000000 INFO @ Tue, 02 Aug 2022 11:55:59: 17000000 INFO @ Tue, 02 Aug 2022 11:56:00: 16000000 INFO @ Tue, 02 Aug 2022 11:56:04: 19000000 INFO @ Tue, 02 Aug 2022 11:56:11: 17000000 INFO @ Tue, 02 Aug 2022 11:56:11: 18000000 INFO @ Tue, 02 Aug 2022 11:56:18: 20000000 INFO @ Tue, 02 Aug 2022 11:56:22: 18000000 INFO @ Tue, 02 Aug 2022 11:56:23: 19000000 INFO @ Tue, 02 Aug 2022 11:56:31: 21000000 INFO @ Tue, 02 Aug 2022 11:56:33: 19000000 INFO @ Tue, 02 Aug 2022 11:56:36: 20000000 INFO @ Tue, 02 Aug 2022 11:56:44: 20000000 INFO @ Tue, 02 Aug 2022 11:56:45: 22000000 INFO @ Tue, 02 Aug 2022 11:56:48: 21000000 INFO @ Tue, 02 Aug 2022 11:56:56: 21000000 INFO @ Tue, 02 Aug 2022 11:56:59: 23000000 INFO @ Tue, 02 Aug 2022 11:56:59: 22000000 INFO @ Tue, 02 Aug 2022 11:57:06: 22000000 INFO @ Tue, 02 Aug 2022 11:57:12: 23000000 INFO @ Tue, 02 Aug 2022 11:57:13: 24000000 INFO @ Tue, 02 Aug 2022 11:57:18: 23000000 INFO @ Tue, 02 Aug 2022 11:57:24: 24000000 INFO @ Tue, 02 Aug 2022 11:57:27: 25000000 INFO @ Tue, 02 Aug 2022 11:57:30: 24000000 INFO @ Tue, 02 Aug 2022 11:57:37: 25000000 INFO @ Tue, 02 Aug 2022 11:57:41: 25000000 INFO @ Tue, 02 Aug 2022 11:57:42: 26000000 INFO @ Tue, 02 Aug 2022 11:57:49: 26000000 INFO @ Tue, 02 Aug 2022 11:57:54: 26000000 INFO @ Tue, 02 Aug 2022 11:57:57: 27000000 INFO @ Tue, 02 Aug 2022 11:57:59: 27000000 INFO @ Tue, 02 Aug 2022 11:58:06: 27000000 INFO @ Tue, 02 Aug 2022 11:58:10: 28000000 INFO @ Tue, 02 Aug 2022 11:58:10: 28000000 INFO @ Tue, 02 Aug 2022 11:58:17: 28000000 INFO @ Tue, 02 Aug 2022 11:58:21: 29000000 INFO @ Tue, 02 Aug 2022 11:58:21: 29000000 INFO @ Tue, 02 Aug 2022 11:58:27: 29000000 INFO @ Tue, 02 Aug 2022 11:58:32: 30000000 INFO @ Tue, 02 Aug 2022 11:58:32: 30000000 INFO @ Tue, 02 Aug 2022 11:58:38: 30000000 INFO @ Tue, 02 Aug 2022 11:58:44: 31000000 INFO @ Tue, 02 Aug 2022 11:58:44: 31000000 INFO @ Tue, 02 Aug 2022 11:58:49: 31000000 INFO @ Tue, 02 Aug 2022 11:58:56: 32000000 INFO @ Tue, 02 Aug 2022 11:58:56: 32000000 INFO @ Tue, 02 Aug 2022 11:58:58: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 11:58:58: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 11:58:58: #1 total tags in treatment: 9896920 INFO @ Tue, 02 Aug 2022 11:58:58: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:58:58: #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 11:58:58: #1 tags after filtering in treatment: 9450740 INFO @ Tue, 02 Aug 2022 11:58:58: #1 Redundant rate of treatment: 0.05 INFO @ Tue, 02 Aug 2022 11:58:58: #1 finished! INFO @ Tue, 02 Aug 2022 11:58:58: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:58:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:58:58: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 11:58:58: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 11:58:58: #1 total tags in treatment: 9896920 INFO @ Tue, 02 Aug 2022 11:58:58: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:58:58: #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 11:58:58: #1 tags after filtering in treatment: 9450740 INFO @ Tue, 02 Aug 2022 11:58:58: #1 Redundant rate of treatment: 0.05 INFO @ Tue, 02 Aug 2022 11:58:58: #1 finished! INFO @ Tue, 02 Aug 2022 11:58:58: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:58:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:58:59: #2 number of paired peaks: 235 WARNING @ Tue, 02 Aug 2022 11:58:59: Fewer paired peaks (235) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 235 pairs to build model! INFO @ Tue, 02 Aug 2022 11:58:59: start model_add_line... INFO @ Tue, 02 Aug 2022 11:58:59: start X-correlation... INFO @ Tue, 02 Aug 2022 11:58:59: #2 number of paired peaks: 235 WARNING @ Tue, 02 Aug 2022 11:58:59: Fewer paired peaks (235) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 235 pairs to build model! INFO @ Tue, 02 Aug 2022 11:58:59: start model_add_line... INFO @ Tue, 02 Aug 2022 11:58:59: start X-correlation... INFO @ Tue, 02 Aug 2022 11:58:59: end of X-cor INFO @ Tue, 02 Aug 2022 11:58:59: end of X-cor INFO @ Tue, 02 Aug 2022 11:58:59: #2 finished! INFO @ Tue, 02 Aug 2022 11:58:59: #2 finished! INFO @ Tue, 02 Aug 2022 11:58:59: #2 predicted fragment length is 227 bps INFO @ Tue, 02 Aug 2022 11:58:59: #2 alternative fragment length(s) may be 227 bps INFO @ Tue, 02 Aug 2022 11:58:59: #2 predicted fragment length is 227 bps INFO @ Tue, 02 Aug 2022 11:58:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13336910/SRX13336910.10_model.r INFO @ Tue, 02 Aug 2022 11:58:59: #2 alternative fragment length(s) may be 227 bps INFO @ Tue, 02 Aug 2022 11:58:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13336910/SRX13336910.05_model.r WARNING @ Tue, 02 Aug 2022 11:58:59: #2 Since the d (227) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:58:59: #2 You may need to consider one of the other alternative d(s): 227 WARNING @ Tue, 02 Aug 2022 11:58:59: #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 11:58:59: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:58:59: #3 Pre-compute pvalue-qvalue table... WARNING @ Tue, 02 Aug 2022 11:58:59: #2 Since the d (227) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:58:59: #2 You may need to consider one of the other alternative d(s): 227 WARNING @ Tue, 02 Aug 2022 11:58:59: #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 11:58:59: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:58:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:59:00: 32000000 INFO @ Tue, 02 Aug 2022 11:59:02: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 11:59:02: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 11:59:02: #1 total tags in treatment: 9896920 INFO @ Tue, 02 Aug 2022 11:59:02: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:59:02: #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 11:59:02: #1 tags after filtering in treatment: 9450740 INFO @ Tue, 02 Aug 2022 11:59:02: #1 Redundant rate of treatment: 0.05 INFO @ Tue, 02 Aug 2022 11:59:02: #1 finished! INFO @ Tue, 02 Aug 2022 11:59:02: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:59:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:59:03: #2 number of paired peaks: 235 WARNING @ Tue, 02 Aug 2022 11:59:03: Fewer paired peaks (235) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 235 pairs to build model! INFO @ Tue, 02 Aug 2022 11:59:03: start model_add_line... INFO @ Tue, 02 Aug 2022 11:59:03: start X-correlation... INFO @ Tue, 02 Aug 2022 11:59:03: end of X-cor INFO @ Tue, 02 Aug 2022 11:59:03: #2 finished! INFO @ Tue, 02 Aug 2022 11:59:03: #2 predicted fragment length is 227 bps INFO @ Tue, 02 Aug 2022 11:59:03: #2 alternative fragment length(s) may be 227 bps INFO @ Tue, 02 Aug 2022 11:59:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13336910/SRX13336910.20_model.r WARNING @ Tue, 02 Aug 2022 11:59:03: #2 Since the d (227) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:59:03: #2 You may need to consider one of the other alternative d(s): 227 WARNING @ Tue, 02 Aug 2022 11:59:03: #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 11:59:03: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:59:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:59:26: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:59:28: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:59:29: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:59:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13336910/SRX13336910.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:59:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13336910/SRX13336910.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:59:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13336910/SRX13336910.05_summits.bed INFO @ Tue, 02 Aug 2022 11:59:39: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (408 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:59:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13336910/SRX13336910.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:59:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13336910/SRX13336910.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:59:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13336910/SRX13336910.20_summits.bed INFO @ Tue, 02 Aug 2022 11:59:41: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (196 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:59:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13336910/SRX13336910.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:59:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13336910/SRX13336910.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:59:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13336910/SRX13336910.10_summits.bed INFO @ Tue, 02 Aug 2022 11:59:42: Done! pass1 - making usageList (6 chroms): 10 millis pass2 - checking and writing primary data (292 records, 4 fields): 22 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。