Job ID = 16435511 SRX = SRX13336909 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: 00:44:42 25158842 reads; of these: 25158842 (100.00%) were paired; of these: 11608415 (46.14%) aligned concordantly 0 times 11467286 (45.58%) aligned concordantly exactly 1 time 2083141 (8.28%) aligned concordantly >1 times ---- 11608415 pairs aligned concordantly 0 times; of these: 5557843 (47.88%) aligned discordantly 1 time ---- 6050572 pairs aligned 0 times concordantly or discordantly; of these: 12101144 mates make up the pairs; of these: 10053868 (83.08%) aligned 0 times 906044 (7.49%) aligned exactly 1 time 1141232 (9.43%) aligned >1 times 80.02% overall alignment rate Time searching: 00:44:42 Overall time: 00:44:42 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 32 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] 2377827 / 19049421 = 0.1248 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 11:47:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13336909/SRX13336909.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13336909/SRX13336909.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13336909/SRX13336909.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13336909/SRX13336909.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 11:47:47: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:47:47: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:47:55: 1000000 INFO @ Tue, 02 Aug 2022 11:48:02: 2000000 INFO @ Tue, 02 Aug 2022 11:48:10: 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 11:48:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13336909/SRX13336909.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13336909/SRX13336909.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13336909/SRX13336909.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13336909/SRX13336909.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 11:48:16: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:48:16: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:48:18: 4000000 INFO @ Tue, 02 Aug 2022 11:48:24: 1000000 INFO @ Tue, 02 Aug 2022 11:48:26: 5000000 INFO @ Tue, 02 Aug 2022 11:48:33: 2000000 INFO @ Tue, 02 Aug 2022 11:48:34: 6000000 INFO @ Tue, 02 Aug 2022 11:48:41: 3000000 INFO @ Tue, 02 Aug 2022 11:48:43: 7000000 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 11:48:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13336909/SRX13336909.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13336909/SRX13336909.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13336909/SRX13336909.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13336909/SRX13336909.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 11:48:46: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:48:46: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:48:50: 4000000 INFO @ Tue, 02 Aug 2022 11:48:52: 8000000 INFO @ Tue, 02 Aug 2022 11:48:55: 1000000 INFO @ Tue, 02 Aug 2022 11:48:59: 5000000 INFO @ Tue, 02 Aug 2022 11:49:01: 9000000 INFO @ Tue, 02 Aug 2022 11:49:04: 2000000 INFO @ Tue, 02 Aug 2022 11:49:08: 6000000 INFO @ Tue, 02 Aug 2022 11:49:10: 10000000 INFO @ Tue, 02 Aug 2022 11:49:13: 3000000 INFO @ Tue, 02 Aug 2022 11:49:16: 7000000 INFO @ Tue, 02 Aug 2022 11:49:18: 11000000 INFO @ Tue, 02 Aug 2022 11:49:22: 4000000 INFO @ Tue, 02 Aug 2022 11:49:25: 8000000 INFO @ Tue, 02 Aug 2022 11:49:27: 12000000 INFO @ Tue, 02 Aug 2022 11:49:31: 5000000 INFO @ Tue, 02 Aug 2022 11:49:34: 9000000 INFO @ Tue, 02 Aug 2022 11:49:36: 13000000 INFO @ Tue, 02 Aug 2022 11:49:39: 6000000 INFO @ Tue, 02 Aug 2022 11:49:42: 10000000 INFO @ Tue, 02 Aug 2022 11:49:45: 14000000 INFO @ Tue, 02 Aug 2022 11:49:48: 7000000 INFO @ Tue, 02 Aug 2022 11:49:51: 11000000 INFO @ Tue, 02 Aug 2022 11:49:53: 15000000 INFO @ Tue, 02 Aug 2022 11:49:56: 8000000 INFO @ Tue, 02 Aug 2022 11:50:00: 12000000 INFO @ Tue, 02 Aug 2022 11:50:02: 16000000 INFO @ Tue, 02 Aug 2022 11:50:05: 9000000 INFO @ Tue, 02 Aug 2022 11:50:08: 13000000 INFO @ Tue, 02 Aug 2022 11:50:11: 17000000 INFO @ Tue, 02 Aug 2022 11:50:13: 10000000 INFO @ Tue, 02 Aug 2022 11:50:17: 14000000 INFO @ Tue, 02 Aug 2022 11:50:19: 18000000 INFO @ Tue, 02 Aug 2022 11:50:22: 11000000 INFO @ Tue, 02 Aug 2022 11:50:25: 15000000 INFO @ Tue, 02 Aug 2022 11:50:28: 19000000 INFO @ Tue, 02 Aug 2022 11:50:30: 12000000 INFO @ Tue, 02 Aug 2022 11:50:34: 16000000 INFO @ Tue, 02 Aug 2022 11:50:36: 20000000 INFO @ Tue, 02 Aug 2022 11:50:39: 13000000 INFO @ Tue, 02 Aug 2022 11:50:42: 17000000 INFO @ Tue, 02 Aug 2022 11:50:45: 21000000 INFO @ Tue, 02 Aug 2022 11:50:47: 14000000 INFO @ Tue, 02 Aug 2022 11:50:50: 18000000 INFO @ Tue, 02 Aug 2022 11:50:53: 22000000 INFO @ Tue, 02 Aug 2022 11:50:56: 15000000 INFO @ Tue, 02 Aug 2022 11:50:59: 19000000 INFO @ Tue, 02 Aug 2022 11:51:03: 23000000 INFO @ Tue, 02 Aug 2022 11:51:06: 16000000 INFO @ Tue, 02 Aug 2022 11:51:09: 20000000 INFO @ Tue, 02 Aug 2022 11:51:12: 24000000 INFO @ Tue, 02 Aug 2022 11:51:15: 17000000 INFO @ Tue, 02 Aug 2022 11:51:17: 21000000 INFO @ Tue, 02 Aug 2022 11:51:21: 25000000 INFO @ Tue, 02 Aug 2022 11:51:24: 18000000 INFO @ Tue, 02 Aug 2022 11:51:26: 22000000 INFO @ Tue, 02 Aug 2022 11:51:29: 26000000 INFO @ Tue, 02 Aug 2022 11:51:32: 19000000 INFO @ Tue, 02 Aug 2022 11:51:34: 23000000 INFO @ Tue, 02 Aug 2022 11:51:38: 27000000 INFO @ Tue, 02 Aug 2022 11:51:41: 20000000 INFO @ Tue, 02 Aug 2022 11:51:43: 24000000 INFO @ Tue, 02 Aug 2022 11:51:46: 28000000 INFO @ Tue, 02 Aug 2022 11:51:49: 21000000 INFO @ Tue, 02 Aug 2022 11:51:51: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 11:51:55: 29000000 INFO @ Tue, 02 Aug 2022 11:51:58: 22000000 INFO @ Tue, 02 Aug 2022 11:51:59: 26000000 INFO @ Tue, 02 Aug 2022 11:52:03: 30000000 INFO @ Tue, 02 Aug 2022 11:52:06: 23000000 INFO @ Tue, 02 Aug 2022 11:52:08: 27000000 INFO @ Tue, 02 Aug 2022 11:52:12: 31000000 INFO @ Tue, 02 Aug 2022 11:52:14: 24000000 INFO @ Tue, 02 Aug 2022 11:52:16: 28000000 INFO @ Tue, 02 Aug 2022 11:52:20: 32000000 INFO @ Tue, 02 Aug 2022 11:52:23: 25000000 INFO @ Tue, 02 Aug 2022 11:52:24: 29000000 INFO @ Tue, 02 Aug 2022 11:52:28: 33000000 INFO @ Tue, 02 Aug 2022 11:52:31: 26000000 INFO @ Tue, 02 Aug 2022 11:52:32: 30000000 INFO @ Tue, 02 Aug 2022 11:52:37: 34000000 INFO @ Tue, 02 Aug 2022 11:52:40: 27000000 INFO @ Tue, 02 Aug 2022 11:52:41: 31000000 INFO @ Tue, 02 Aug 2022 11:52:45: 35000000 INFO @ Tue, 02 Aug 2022 11:52:49: 28000000 INFO @ Tue, 02 Aug 2022 11:52:50: 32000000 INFO @ Tue, 02 Aug 2022 11:52:50: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 11:52:50: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 11:52:50: #1 total tags in treatment: 11753107 INFO @ Tue, 02 Aug 2022 11:52:50: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:52:50: #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 11:52:50: #1 tags after filtering in treatment: 10731102 INFO @ Tue, 02 Aug 2022 11:52:50: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 02 Aug 2022 11:52:50: #1 finished! INFO @ Tue, 02 Aug 2022 11:52:50: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:52:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:52:51: #2 number of paired peaks: 451 WARNING @ Tue, 02 Aug 2022 11:52:51: Fewer paired peaks (451) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 451 pairs to build model! INFO @ Tue, 02 Aug 2022 11:52:51: start model_add_line... INFO @ Tue, 02 Aug 2022 11:52:51: start X-correlation... INFO @ Tue, 02 Aug 2022 11:52:51: end of X-cor INFO @ Tue, 02 Aug 2022 11:52:51: #2 finished! INFO @ Tue, 02 Aug 2022 11:52:51: #2 predicted fragment length is 219 bps INFO @ Tue, 02 Aug 2022 11:52:51: #2 alternative fragment length(s) may be 219 bps INFO @ Tue, 02 Aug 2022 11:52:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13336909/SRX13336909.05_model.r WARNING @ Tue, 02 Aug 2022 11:52:51: #2 Since the d (219) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:52:51: #2 You may need to consider one of the other alternative d(s): 219 WARNING @ Tue, 02 Aug 2022 11:52:51: #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 11:52:51: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:52:51: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 11:52:58: 29000000 INFO @ Tue, 02 Aug 2022 11:52:58: 33000000 INFO @ Tue, 02 Aug 2022 11:53:06: 34000000 INFO @ Tue, 02 Aug 2022 11:53:06: 30000000 INFO @ Tue, 02 Aug 2022 11:53:13: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:53:15: 35000000 INFO @ Tue, 02 Aug 2022 11:53:15: 31000000 INFO @ Tue, 02 Aug 2022 11:53:19: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 11:53:19: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 11:53:19: #1 total tags in treatment: 11753107 INFO @ Tue, 02 Aug 2022 11:53:19: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:53:19: #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 11:53:20: #1 tags after filtering in treatment: 10731102 INFO @ Tue, 02 Aug 2022 11:53:20: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 02 Aug 2022 11:53:20: #1 finished! INFO @ Tue, 02 Aug 2022 11:53:20: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:53:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:53:20: #2 number of paired peaks: 451 WARNING @ Tue, 02 Aug 2022 11:53:20: Fewer paired peaks (451) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 451 pairs to build model! INFO @ Tue, 02 Aug 2022 11:53:20: start model_add_line... INFO @ Tue, 02 Aug 2022 11:53:20: start X-correlation... INFO @ Tue, 02 Aug 2022 11:53:20: end of X-cor INFO @ Tue, 02 Aug 2022 11:53:20: #2 finished! INFO @ Tue, 02 Aug 2022 11:53:20: #2 predicted fragment length is 219 bps INFO @ Tue, 02 Aug 2022 11:53:20: #2 alternative fragment length(s) may be 219 bps INFO @ Tue, 02 Aug 2022 11:53:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13336909/SRX13336909.10_model.r WARNING @ Tue, 02 Aug 2022 11:53:20: #2 Since the d (219) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:53:20: #2 You may need to consider one of the other alternative d(s): 219 WARNING @ Tue, 02 Aug 2022 11:53:20: #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 11:53:20: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:53:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:53:23: 32000000 INFO @ Tue, 02 Aug 2022 11:53:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13336909/SRX13336909.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:53:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13336909/SRX13336909.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:53:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13336909/SRX13336909.05_summits.bed INFO @ Tue, 02 Aug 2022 11:53:23: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (493 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:53:31: 33000000 INFO @ Tue, 02 Aug 2022 11:53:38: 34000000 INFO @ Tue, 02 Aug 2022 11:53:43: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:53:45: 35000000 INFO @ Tue, 02 Aug 2022 11:53:49: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 11:53:49: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 11:53:49: #1 total tags in treatment: 11753107 INFO @ Tue, 02 Aug 2022 11:53:49: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:53:49: #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 11:53:49: #1 tags after filtering in treatment: 10731102 INFO @ Tue, 02 Aug 2022 11:53:49: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 02 Aug 2022 11:53:49: #1 finished! INFO @ Tue, 02 Aug 2022 11:53:49: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:53:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:53:50: #2 number of paired peaks: 451 WARNING @ Tue, 02 Aug 2022 11:53:50: Fewer paired peaks (451) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 451 pairs to build model! INFO @ Tue, 02 Aug 2022 11:53:50: start model_add_line... INFO @ Tue, 02 Aug 2022 11:53:50: start X-correlation... INFO @ Tue, 02 Aug 2022 11:53:50: end of X-cor INFO @ Tue, 02 Aug 2022 11:53:50: #2 finished! INFO @ Tue, 02 Aug 2022 11:53:50: #2 predicted fragment length is 219 bps INFO @ Tue, 02 Aug 2022 11:53:50: #2 alternative fragment length(s) may be 219 bps INFO @ Tue, 02 Aug 2022 11:53:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13336909/SRX13336909.20_model.r WARNING @ Tue, 02 Aug 2022 11:53:50: #2 Since the d (219) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:53:50: #2 You may need to consider one of the other alternative d(s): 219 WARNING @ Tue, 02 Aug 2022 11:53:50: #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 11:53:50: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:53:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:53:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13336909/SRX13336909.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:53:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13336909/SRX13336909.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:53:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13336909/SRX13336909.10_summits.bed INFO @ Tue, 02 Aug 2022 11:53:53: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (393 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:54:12: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:54:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13336909/SRX13336909.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:54:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13336909/SRX13336909.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:54:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13336909/SRX13336909.20_summits.bed INFO @ Tue, 02 Aug 2022 11:54:22: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (280 records, 4 fields): 55 millis CompletedMACS2peakCalling