Job ID = 16432963 SRX = SRX13336912 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 21758942 spots for SRR17152876/SRR17152876.sra Written 21758942 spots for SRR17152876/SRR17152876.sra fastq に変換しました。 bowtie でマッピング中... Your job 16435019 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:50:25 21758942 reads; of these: 21758942 (100.00%) were paired; of these: 9116650 (41.90%) aligned concordantly 0 times 10798439 (49.63%) aligned concordantly exactly 1 time 1843853 (8.47%) aligned concordantly >1 times ---- 9116650 pairs aligned concordantly 0 times; of these: 3663120 (40.18%) aligned discordantly 1 time ---- 5453530 pairs aligned 0 times concordantly or discordantly; of these: 10907060 mates make up the pairs; of these: 9611567 (88.12%) aligned 0 times 577514 (5.29%) aligned exactly 1 time 717979 (6.58%) aligned >1 times 77.91% overall alignment rate Time searching: 00:50:25 Overall time: 00:50:25 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] 1446867 / 16234235 = 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 10:50:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13336912/SRX13336912.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13336912/SRX13336912.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13336912/SRX13336912.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 10:50:13: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:50:13: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:50:20: 1000000 INFO @ Tue, 02 Aug 2022 10:50:28: 2000000 INFO @ Tue, 02 Aug 2022 10:50:36: 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 10:50:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13336912/SRX13336912.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13336912/SRX13336912.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13336912/SRX13336912.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 10:50:42: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:50:42: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:50:44: 4000000 INFO @ Tue, 02 Aug 2022 10:50:52: 1000000 INFO @ Tue, 02 Aug 2022 10:50:53: 5000000 INFO @ Tue, 02 Aug 2022 10:51:01: 6000000 INFO @ Tue, 02 Aug 2022 10:51:02: 2000000 INFO @ Tue, 02 Aug 2022 10:51:09: 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 10:51:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13336912/SRX13336912.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13336912/SRX13336912.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13336912/SRX13336912.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 10:51:12: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:51:12: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:51:13: 3000000 INFO @ Tue, 02 Aug 2022 10:51:20: 8000000 INFO @ Tue, 02 Aug 2022 10:51:22: 1000000 INFO @ Tue, 02 Aug 2022 10:51:23: 4000000 INFO @ Tue, 02 Aug 2022 10:51:32: 2000000 INFO @ Tue, 02 Aug 2022 10:51:34: 5000000 INFO @ Tue, 02 Aug 2022 10:51:34: 9000000 INFO @ Tue, 02 Aug 2022 10:51:42: 3000000 INFO @ Tue, 02 Aug 2022 10:51:44: 6000000 INFO @ Tue, 02 Aug 2022 10:51:46: 10000000 INFO @ Tue, 02 Aug 2022 10:51:53: 4000000 INFO @ Tue, 02 Aug 2022 10:51:54: 7000000 INFO @ Tue, 02 Aug 2022 10:51:57: 11000000 INFO @ Tue, 02 Aug 2022 10:52:04: 5000000 INFO @ Tue, 02 Aug 2022 10:52:04: 8000000 INFO @ Tue, 02 Aug 2022 10:52:07: 12000000 INFO @ Tue, 02 Aug 2022 10:52:14: 9000000 INFO @ Tue, 02 Aug 2022 10:52:15: 6000000 INFO @ Tue, 02 Aug 2022 10:52:18: 13000000 INFO @ Tue, 02 Aug 2022 10:52:24: 10000000 INFO @ Tue, 02 Aug 2022 10:52:25: 7000000 INFO @ Tue, 02 Aug 2022 10:52:29: 14000000 INFO @ Tue, 02 Aug 2022 10:52:35: 11000000 INFO @ Tue, 02 Aug 2022 10:52:36: 8000000 INFO @ Tue, 02 Aug 2022 10:52:41: 15000000 INFO @ Tue, 02 Aug 2022 10:52:45: 12000000 INFO @ Tue, 02 Aug 2022 10:52:46: 9000000 INFO @ Tue, 02 Aug 2022 10:52:55: 16000000 INFO @ Tue, 02 Aug 2022 10:52:55: 13000000 INFO @ Tue, 02 Aug 2022 10:52:55: 10000000 INFO @ Tue, 02 Aug 2022 10:53:05: 11000000 INFO @ Tue, 02 Aug 2022 10:53:06: 14000000 INFO @ Tue, 02 Aug 2022 10:53:10: 17000000 INFO @ Tue, 02 Aug 2022 10:53:15: 12000000 INFO @ Tue, 02 Aug 2022 10:53:17: 15000000 INFO @ Tue, 02 Aug 2022 10:53:22: 18000000 INFO @ Tue, 02 Aug 2022 10:53:25: 13000000 INFO @ Tue, 02 Aug 2022 10:53:26: 16000000 INFO @ Tue, 02 Aug 2022 10:53:33: 19000000 INFO @ Tue, 02 Aug 2022 10:53:35: 17000000 INFO @ Tue, 02 Aug 2022 10:53:37: 14000000 INFO @ Tue, 02 Aug 2022 10:53:46: 18000000 INFO @ Tue, 02 Aug 2022 10:53:47: 20000000 INFO @ Tue, 02 Aug 2022 10:53:47: 15000000 INFO @ Tue, 02 Aug 2022 10:53:57: 16000000 INFO @ Tue, 02 Aug 2022 10:53:57: 19000000 INFO @ Tue, 02 Aug 2022 10:54:01: 21000000 INFO @ Tue, 02 Aug 2022 10:54:08: 20000000 INFO @ Tue, 02 Aug 2022 10:54:08: 17000000 INFO @ Tue, 02 Aug 2022 10:54:11: 22000000 INFO @ Tue, 02 Aug 2022 10:54:18: 21000000 INFO @ Tue, 02 Aug 2022 10:54:18: 18000000 INFO @ Tue, 02 Aug 2022 10:54:20: 23000000 INFO @ Tue, 02 Aug 2022 10:54:28: 22000000 INFO @ Tue, 02 Aug 2022 10:54:29: 19000000 INFO @ Tue, 02 Aug 2022 10:54:30: 24000000 INFO @ Tue, 02 Aug 2022 10:54:38: 23000000 INFO @ Tue, 02 Aug 2022 10:54:40: 20000000 INFO @ Tue, 02 Aug 2022 10:54:41: 25000000 INFO @ Tue, 02 Aug 2022 10:54:48: 24000000 INFO @ Tue, 02 Aug 2022 10:54:51: 21000000 INFO @ Tue, 02 Aug 2022 10:54:52: 26000000 INFO @ Tue, 02 Aug 2022 10:54:58: 25000000 INFO @ Tue, 02 Aug 2022 10:55:02: 22000000 INFO @ Tue, 02 Aug 2022 10:55:03: 27000000 INFO @ Tue, 02 Aug 2022 10:55:07: 26000000 INFO @ Tue, 02 Aug 2022 10:55:13: 23000000 INFO @ Tue, 02 Aug 2022 10:55:13: 28000000 INFO @ Tue, 02 Aug 2022 10:55:17: 27000000 INFO @ Tue, 02 Aug 2022 10:55:24: 24000000 INFO @ Tue, 02 Aug 2022 10:55:24: 29000000 INFO @ Tue, 02 Aug 2022 10:55:27: 28000000 INFO @ Tue, 02 Aug 2022 10:55:34: 25000000 INFO @ Tue, 02 Aug 2022 10:55:34: 30000000 INFO @ Tue, 02 Aug 2022 10:55:37: 29000000 INFO @ Tue, 02 Aug 2022 10:55:43: 31000000 INFO @ Tue, 02 Aug 2022 10:55:43: 26000000 INFO @ Tue, 02 Aug 2022 10:55:44: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 10:55:44: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 10:55:44: #1 total tags in treatment: 11451560 INFO @ Tue, 02 Aug 2022 10:55:44: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:55:44: #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 10:55:44: #1 tags after filtering in treatment: 10554832 INFO @ Tue, 02 Aug 2022 10:55:44: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 02 Aug 2022 10:55:44: #1 finished! INFO @ Tue, 02 Aug 2022 10:55:44: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:55:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:55:45: #2 number of paired peaks: 440 WARNING @ Tue, 02 Aug 2022 10:55:45: 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 10:55:45: start model_add_line... INFO @ Tue, 02 Aug 2022 10:55:45: start X-correlation... INFO @ Tue, 02 Aug 2022 10:55:45: end of X-cor INFO @ Tue, 02 Aug 2022 10:55:45: #2 finished! INFO @ Tue, 02 Aug 2022 10:55:45: #2 predicted fragment length is 216 bps INFO @ Tue, 02 Aug 2022 10:55:45: #2 alternative fragment length(s) may be 216 bps INFO @ Tue, 02 Aug 2022 10:55:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13336912/SRX13336912.05_model.r WARNING @ Tue, 02 Aug 2022 10:55:45: #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 10:55:45: #2 You may need to consider one of the other alternative d(s): 216 WARNING @ Tue, 02 Aug 2022 10:55:45: #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 10:55:45: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:55:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:55:48: 30000000 INFO @ Tue, 02 Aug 2022 10:55:52: 27000000 INFO @ Tue, 02 Aug 2022 10:55:59: 31000000 INFO @ Tue, 02 Aug 2022 10:56:00: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 10:56:00: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 10:56:00: #1 total tags in treatment: 11451560 INFO @ Tue, 02 Aug 2022 10:56:00: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:56:00: #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 10:56:00: #1 tags after filtering in treatment: 10554832 INFO @ Tue, 02 Aug 2022 10:56:00: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 02 Aug 2022 10:56:00: #1 finished! INFO @ Tue, 02 Aug 2022 10:56:00: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:56:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:56:01: #2 number of paired peaks: 440 WARNING @ Tue, 02 Aug 2022 10:56:01: 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 10:56:01: start model_add_line... INFO @ Tue, 02 Aug 2022 10:56:01: 28000000 INFO @ Tue, 02 Aug 2022 10:56:01: start X-correlation... INFO @ Tue, 02 Aug 2022 10:56:01: end of X-cor INFO @ Tue, 02 Aug 2022 10:56:01: #2 finished! INFO @ Tue, 02 Aug 2022 10:56:01: #2 predicted fragment length is 216 bps INFO @ Tue, 02 Aug 2022 10:56:01: #2 alternative fragment length(s) may be 216 bps INFO @ Tue, 02 Aug 2022 10:56:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13336912/SRX13336912.10_model.r WARNING @ Tue, 02 Aug 2022 10:56:01: #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 10:56:01: #2 You may need to consider one of the other alternative d(s): 216 WARNING @ Tue, 02 Aug 2022 10:56:01: #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 10:56:01: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:56:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:56:07: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:56:09: 29000000 INFO @ Tue, 02 Aug 2022 10:56:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13336912/SRX13336912.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:56:17: 30000000 INFO @ Tue, 02 Aug 2022 10:56:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13336912/SRX13336912.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:56:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13336912/SRX13336912.05_summits.bed INFO @ Tue, 02 Aug 2022 10:56:17: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (466 records, 4 fields): 86 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:56:23: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:56:24: 31000000 INFO @ Tue, 02 Aug 2022 10:56:25: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 10:56:25: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 10:56:25: #1 total tags in treatment: 11451560 INFO @ Tue, 02 Aug 2022 10:56:25: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:56:25: #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 10:56:25: #1 tags after filtering in treatment: 10554832 INFO @ Tue, 02 Aug 2022 10:56:25: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 02 Aug 2022 10:56:25: #1 finished! INFO @ Tue, 02 Aug 2022 10:56:25: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:56:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:56:26: #2 number of paired peaks: 440 WARNING @ Tue, 02 Aug 2022 10:56:26: 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 10:56:26: start model_add_line... INFO @ Tue, 02 Aug 2022 10:56:26: start X-correlation... INFO @ Tue, 02 Aug 2022 10:56:26: end of X-cor INFO @ Tue, 02 Aug 2022 10:56:26: #2 finished! INFO @ Tue, 02 Aug 2022 10:56:26: #2 predicted fragment length is 216 bps INFO @ Tue, 02 Aug 2022 10:56:26: #2 alternative fragment length(s) may be 216 bps INFO @ Tue, 02 Aug 2022 10:56:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13336912/SRX13336912.20_model.r WARNING @ Tue, 02 Aug 2022 10:56:26: #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 10:56:26: #2 You may need to consider one of the other alternative d(s): 216 WARNING @ Tue, 02 Aug 2022 10:56:26: #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 10:56:26: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:56:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:56:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13336912/SRX13336912.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:56:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13336912/SRX13336912.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:56:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13336912/SRX13336912.10_summits.bed INFO @ Tue, 02 Aug 2022 10:56:33: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (362 records, 4 fields): 25 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:56:47: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:56:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13336912/SRX13336912.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:56:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13336912/SRX13336912.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:56:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13336912/SRX13336912.20_summits.bed INFO @ Tue, 02 Aug 2022 10:56:57: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (263 records, 4 fields): 22 millis CompletedMACS2peakCalling BigWig に変換しました。