Job ID = 16435433 SRX = SRX13336899 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: 00:41:04 24013535 reads; of these: 24013535 (100.00%) were paired; of these: 12811549 (53.35%) aligned concordantly 0 times 9386649 (39.09%) aligned concordantly exactly 1 time 1815337 (7.56%) aligned concordantly >1 times ---- 12811549 pairs aligned concordantly 0 times; of these: 6235525 (48.67%) aligned discordantly 1 time ---- 6576024 pairs aligned 0 times concordantly or discordantly; of these: 13152048 mates make up the pairs; of these: 10770160 (81.89%) aligned 0 times 1120439 (8.52%) aligned exactly 1 time 1261449 (9.59%) aligned >1 times 77.57% overall alignment rate Time searching: 00:41:04 Overall time: 00:41:04 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] 2230109 / 17393149 = 0.1282 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 11:41:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13336899/SRX13336899.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13336899/SRX13336899.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13336899/SRX13336899.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13336899/SRX13336899.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 11:41:30: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:41:30: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:41:39: 1000000 INFO @ Tue, 02 Aug 2022 11:41:47: 2000000 INFO @ Tue, 02 Aug 2022 11:41:56: 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 11:41:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13336899/SRX13336899.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13336899/SRX13336899.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13336899/SRX13336899.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13336899/SRX13336899.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 11:41:59: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:41:59: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:42:07: 4000000 INFO @ Tue, 02 Aug 2022 11:42:09: 1000000 INFO @ Tue, 02 Aug 2022 11:42:17: 5000000 INFO @ Tue, 02 Aug 2022 11:42:20: 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 11:42:28: 6000000 INFO @ Tue, 02 Aug 2022 11:42:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13336899/SRX13336899.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13336899/SRX13336899.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13336899/SRX13336899.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13336899/SRX13336899.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 11:42:29: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:42:29: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:42:30: 3000000 INFO @ Tue, 02 Aug 2022 11:42:41: 7000000 INFO @ Tue, 02 Aug 2022 11:42:42: 4000000 INFO @ Tue, 02 Aug 2022 11:42:43: 1000000 INFO @ Tue, 02 Aug 2022 11:42:53: 8000000 INFO @ Tue, 02 Aug 2022 11:42:54: 5000000 INFO @ Tue, 02 Aug 2022 11:42:57: 2000000 INFO @ Tue, 02 Aug 2022 11:43:05: 9000000 INFO @ Tue, 02 Aug 2022 11:43:06: 6000000 INFO @ Tue, 02 Aug 2022 11:43:10: 3000000 INFO @ Tue, 02 Aug 2022 11:43:17: 10000000 INFO @ Tue, 02 Aug 2022 11:43:19: 7000000 INFO @ Tue, 02 Aug 2022 11:43:24: 4000000 INFO @ Tue, 02 Aug 2022 11:43:29: 11000000 INFO @ Tue, 02 Aug 2022 11:43:31: 8000000 INFO @ Tue, 02 Aug 2022 11:43:37: 5000000 INFO @ Tue, 02 Aug 2022 11:43:42: 12000000 INFO @ Tue, 02 Aug 2022 11:43:43: 9000000 INFO @ Tue, 02 Aug 2022 11:43:51: 6000000 INFO @ Tue, 02 Aug 2022 11:43:54: 13000000 INFO @ Tue, 02 Aug 2022 11:43:55: 10000000 INFO @ Tue, 02 Aug 2022 11:44:04: 7000000 INFO @ Tue, 02 Aug 2022 11:44:06: 14000000 INFO @ Tue, 02 Aug 2022 11:44:08: 11000000 INFO @ Tue, 02 Aug 2022 11:44:18: 8000000 INFO @ Tue, 02 Aug 2022 11:44:19: 15000000 INFO @ Tue, 02 Aug 2022 11:44:20: 12000000 INFO @ Tue, 02 Aug 2022 11:44:31: 16000000 INFO @ Tue, 02 Aug 2022 11:44:32: 9000000 INFO @ Tue, 02 Aug 2022 11:44:32: 13000000 INFO @ Tue, 02 Aug 2022 11:44:43: 17000000 INFO @ Tue, 02 Aug 2022 11:44:45: 14000000 INFO @ Tue, 02 Aug 2022 11:44:45: 10000000 INFO @ Tue, 02 Aug 2022 11:44:56: 18000000 INFO @ Tue, 02 Aug 2022 11:44:57: 15000000 INFO @ Tue, 02 Aug 2022 11:44:59: 11000000 INFO @ Tue, 02 Aug 2022 11:45:09: 19000000 INFO @ Tue, 02 Aug 2022 11:45:10: 16000000 INFO @ Tue, 02 Aug 2022 11:45:13: 12000000 INFO @ Tue, 02 Aug 2022 11:45:21: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 11:45:22: 17000000 INFO @ Tue, 02 Aug 2022 11:45:26: 13000000 INFO @ Tue, 02 Aug 2022 11:45:34: 21000000 INFO @ Tue, 02 Aug 2022 11:45:35: 18000000 INFO @ Tue, 02 Aug 2022 11:45:40: 14000000 INFO @ Tue, 02 Aug 2022 11:45:46: 22000000 INFO @ Tue, 02 Aug 2022 11:45:47: 19000000 INFO @ Tue, 02 Aug 2022 11:45:53: 15000000 INFO @ Tue, 02 Aug 2022 11:45:59: 23000000 INFO @ Tue, 02 Aug 2022 11:45:59: 20000000 INFO @ Tue, 02 Aug 2022 11:46:07: 16000000 INFO @ Tue, 02 Aug 2022 11:46:11: 24000000 INFO @ Tue, 02 Aug 2022 11:46:12: 21000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 11:46:21: 17000000 INFO @ Tue, 02 Aug 2022 11:46:23: 25000000 INFO @ Tue, 02 Aug 2022 11:46:24: 22000000 INFO @ Tue, 02 Aug 2022 11:46:34: 18000000 INFO @ Tue, 02 Aug 2022 11:46:36: 26000000 INFO @ Tue, 02 Aug 2022 11:46:36: 23000000 INFO @ Tue, 02 Aug 2022 11:46:48: 19000000 INFO @ Tue, 02 Aug 2022 11:46:48: 27000000 INFO @ Tue, 02 Aug 2022 11:46:48: 24000000 INFO @ Tue, 02 Aug 2022 11:47:01: 28000000 INFO @ Tue, 02 Aug 2022 11:47:01: 25000000 INFO @ Tue, 02 Aug 2022 11:47:01: 20000000 INFO @ Tue, 02 Aug 2022 11:47:13: 29000000 INFO @ Tue, 02 Aug 2022 11:47:13: 26000000 INFO @ Tue, 02 Aug 2022 11:47:15: 21000000 INFO @ Tue, 02 Aug 2022 11:47:25: 30000000 INFO @ Tue, 02 Aug 2022 11:47:25: 27000000 INFO @ Tue, 02 Aug 2022 11:47:28: 22000000 INFO @ Tue, 02 Aug 2022 11:47:37: 31000000 INFO @ Tue, 02 Aug 2022 11:47:37: 28000000 INFO @ Tue, 02 Aug 2022 11:47:42: 23000000 INFO @ Tue, 02 Aug 2022 11:47:49: 32000000 INFO @ Tue, 02 Aug 2022 11:47:50: 29000000 INFO @ Tue, 02 Aug 2022 11:47:55: 24000000 INFO @ Tue, 02 Aug 2022 11:47:59: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 11:47:59: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 11:47:59: #1 total tags in treatment: 9648986 INFO @ Tue, 02 Aug 2022 11:47:59: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:47:59: #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 11:47:59: #1 tags after filtering in treatment: 8763983 INFO @ Tue, 02 Aug 2022 11:47:59: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 02 Aug 2022 11:47:59: #1 finished! INFO @ Tue, 02 Aug 2022 11:47:59: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:47:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:48:00: #2 number of paired peaks: 569 WARNING @ Tue, 02 Aug 2022 11:48:00: Fewer paired peaks (569) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 569 pairs to build model! INFO @ Tue, 02 Aug 2022 11:48:00: start model_add_line... INFO @ Tue, 02 Aug 2022 11:48:00: start X-correlation... INFO @ Tue, 02 Aug 2022 11:48:00: end of X-cor INFO @ Tue, 02 Aug 2022 11:48:00: #2 finished! INFO @ Tue, 02 Aug 2022 11:48:00: #2 predicted fragment length is 223 bps INFO @ Tue, 02 Aug 2022 11:48:00: #2 alternative fragment length(s) may be 223 bps INFO @ Tue, 02 Aug 2022 11:48:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13336899/SRX13336899.05_model.r WARNING @ Tue, 02 Aug 2022 11:48:00: #2 Since the d (223) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:48:00: #2 You may need to consider one of the other alternative d(s): 223 WARNING @ Tue, 02 Aug 2022 11:48:00: #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 11:48:00: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:48:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:48:02: 30000000 INFO @ Tue, 02 Aug 2022 11:48:08: 25000000 INFO @ Tue, 02 Aug 2022 11:48:14: 31000000 INFO @ Tue, 02 Aug 2022 11:48:19: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:48:22: 26000000 INFO @ Tue, 02 Aug 2022 11:48:25: 32000000 INFO @ Tue, 02 Aug 2022 11:48:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13336899/SRX13336899.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:48:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13336899/SRX13336899.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:48:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13336899/SRX13336899.05_summits.bed INFO @ Tue, 02 Aug 2022 11:48:28: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (502 records, 4 fields): 91 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:48:35: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 11:48:35: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 11:48:35: #1 total tags in treatment: 9648986 INFO @ Tue, 02 Aug 2022 11:48:35: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:48:35: #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 11:48:35: #1 tags after filtering in treatment: 8763983 INFO @ Tue, 02 Aug 2022 11:48:35: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 02 Aug 2022 11:48:35: #1 finished! INFO @ Tue, 02 Aug 2022 11:48:35: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:48:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:48:35: 27000000 INFO @ Tue, 02 Aug 2022 11:48:35: #2 number of paired peaks: 569 WARNING @ Tue, 02 Aug 2022 11:48:35: Fewer paired peaks (569) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 569 pairs to build model! INFO @ Tue, 02 Aug 2022 11:48:35: start model_add_line... INFO @ Tue, 02 Aug 2022 11:48:35: start X-correlation... INFO @ Tue, 02 Aug 2022 11:48:35: end of X-cor INFO @ Tue, 02 Aug 2022 11:48:35: #2 finished! INFO @ Tue, 02 Aug 2022 11:48:35: #2 predicted fragment length is 223 bps INFO @ Tue, 02 Aug 2022 11:48:35: #2 alternative fragment length(s) may be 223 bps INFO @ Tue, 02 Aug 2022 11:48:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13336899/SRX13336899.10_model.r WARNING @ Tue, 02 Aug 2022 11:48:36: #2 Since the d (223) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:48:36: #2 You may need to consider one of the other alternative d(s): 223 WARNING @ Tue, 02 Aug 2022 11:48:36: #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 11:48:36: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:48:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:48:47: 28000000 INFO @ Tue, 02 Aug 2022 11:48:55: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:48:59: 29000000 INFO @ Tue, 02 Aug 2022 11:49:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13336899/SRX13336899.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:49:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13336899/SRX13336899.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:49:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13336899/SRX13336899.10_summits.bed INFO @ Tue, 02 Aug 2022 11:49:04: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (395 records, 4 fields): 96 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:49:10: 30000000 INFO @ Tue, 02 Aug 2022 11:49:22: 31000000 INFO @ Tue, 02 Aug 2022 11:49:34: 32000000 INFO @ Tue, 02 Aug 2022 11:49:43: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 11:49:43: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 11:49:43: #1 total tags in treatment: 9648986 INFO @ Tue, 02 Aug 2022 11:49:43: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:49:43: #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 11:49:43: #1 tags after filtering in treatment: 8763983 INFO @ Tue, 02 Aug 2022 11:49:43: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 02 Aug 2022 11:49:43: #1 finished! INFO @ Tue, 02 Aug 2022 11:49:43: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:49:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:49:43: #2 number of paired peaks: 569 WARNING @ Tue, 02 Aug 2022 11:49:43: Fewer paired peaks (569) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 569 pairs to build model! INFO @ Tue, 02 Aug 2022 11:49:43: start model_add_line... INFO @ Tue, 02 Aug 2022 11:49:43: start X-correlation... INFO @ Tue, 02 Aug 2022 11:49:43: end of X-cor INFO @ Tue, 02 Aug 2022 11:49:43: #2 finished! INFO @ Tue, 02 Aug 2022 11:49:43: #2 predicted fragment length is 223 bps INFO @ Tue, 02 Aug 2022 11:49:43: #2 alternative fragment length(s) may be 223 bps INFO @ Tue, 02 Aug 2022 11:49:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13336899/SRX13336899.20_model.r WARNING @ Tue, 02 Aug 2022 11:49:44: #2 Since the d (223) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:49:44: #2 You may need to consider one of the other alternative d(s): 223 WARNING @ Tue, 02 Aug 2022 11:49:44: #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 11:49:44: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:49:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:50:02: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:50:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13336899/SRX13336899.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:50:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13336899/SRX13336899.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:50:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13336899/SRX13336899.20_summits.bed INFO @ Tue, 02 Aug 2022 11:50:11: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (288 records, 4 fields): 60 millis CompletedMACS2peakCalling