Job ID = 14159598 SRX = SRX3180777 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 15907059 spots for SRR6030428/SRR6030428.sra Written 15907059 spots for SRR6030428/SRR6030428.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160032 ("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: 00:03:23 15907059 reads; of these: 15907059 (100.00%) were unpaired; of these: 299599 (1.88%) aligned 0 times 12695329 (79.81%) aligned exactly 1 time 2912131 (18.31%) aligned >1 times 98.12% overall alignment rate Time searching: 00:03:23 Overall time: 00:03:23 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 8 files... [bam_rmdupse_core] 2262179 / 15607460 = 0.1449 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 23:19:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180777/SRX3180777.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180777/SRX3180777.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180777/SRX3180777.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180777/SRX3180777.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 @ Wed, 08 Dec 2021 23:19:17: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:19:17: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:19:23: 1000000 INFO @ Wed, 08 Dec 2021 23:19:29: 2000000 INFO @ Wed, 08 Dec 2021 23:19:35: 3000000 INFO @ Wed, 08 Dec 2021 23:19:41: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 23:19:46: 5000000 INFO @ Wed, 08 Dec 2021 23:19:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180777/SRX3180777.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180777/SRX3180777.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180777/SRX3180777.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180777/SRX3180777.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 @ Wed, 08 Dec 2021 23:19:47: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:19:47: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:19:53: 6000000 INFO @ Wed, 08 Dec 2021 23:19:54: 1000000 INFO @ Wed, 08 Dec 2021 23:20:00: 7000000 INFO @ Wed, 08 Dec 2021 23:20:01: 2000000 INFO @ Wed, 08 Dec 2021 23:20:06: 8000000 INFO @ Wed, 08 Dec 2021 23:20:08: 3000000 INFO @ Wed, 08 Dec 2021 23:20:13: 9000000 INFO @ Wed, 08 Dec 2021 23:20:14: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 23:20:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180777/SRX3180777.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180777/SRX3180777.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180777/SRX3180777.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180777/SRX3180777.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 @ Wed, 08 Dec 2021 23:20:17: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:20:17: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:20:20: 10000000 INFO @ Wed, 08 Dec 2021 23:20:21: 5000000 INFO @ Wed, 08 Dec 2021 23:20:24: 1000000 INFO @ Wed, 08 Dec 2021 23:20:27: 11000000 INFO @ Wed, 08 Dec 2021 23:20:28: 6000000 INFO @ Wed, 08 Dec 2021 23:20:31: 2000000 INFO @ Wed, 08 Dec 2021 23:20:34: 12000000 INFO @ Wed, 08 Dec 2021 23:20:35: 7000000 INFO @ Wed, 08 Dec 2021 23:20:38: 3000000 INFO @ Wed, 08 Dec 2021 23:20:40: 13000000 INFO @ Wed, 08 Dec 2021 23:20:41: 8000000 INFO @ Wed, 08 Dec 2021 23:20:43: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 23:20:43: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 23:20:43: #1 total tags in treatment: 13345281 INFO @ Wed, 08 Dec 2021 23:20:43: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:20:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 23:20:43: #1 tags after filtering in treatment: 13345281 INFO @ Wed, 08 Dec 2021 23:20:43: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 23:20:43: #1 finished! INFO @ Wed, 08 Dec 2021 23:20:43: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:20:43: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:20:44: #2 number of paired peaks: 401 WARNING @ Wed, 08 Dec 2021 23:20:44: Fewer paired peaks (401) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 401 pairs to build model! INFO @ Wed, 08 Dec 2021 23:20:44: start model_add_line... INFO @ Wed, 08 Dec 2021 23:20:44: start X-correlation... INFO @ Wed, 08 Dec 2021 23:20:44: end of X-cor INFO @ Wed, 08 Dec 2021 23:20:44: #2 finished! INFO @ Wed, 08 Dec 2021 23:20:44: #2 predicted fragment length is 47 bps INFO @ Wed, 08 Dec 2021 23:20:44: #2 alternative fragment length(s) may be 2,47,531,547,576 bps INFO @ Wed, 08 Dec 2021 23:20:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180777/SRX3180777.05_model.r WARNING @ Wed, 08 Dec 2021 23:20:44: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 23:20:44: #2 You may need to consider one of the other alternative d(s): 2,47,531,547,576 WARNING @ Wed, 08 Dec 2021 23:20:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 23:20:44: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:20:44: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:20:45: 4000000 INFO @ Wed, 08 Dec 2021 23:20:48: 9000000 INFO @ Wed, 08 Dec 2021 23:20:52: 5000000 INFO @ Wed, 08 Dec 2021 23:20:55: 10000000 INFO @ Wed, 08 Dec 2021 23:20:59: 6000000 INFO @ Wed, 08 Dec 2021 23:21:02: 11000000 INFO @ Wed, 08 Dec 2021 23:21:06: 7000000 INFO @ Wed, 08 Dec 2021 23:21:07: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:21:09: 12000000 INFO @ Wed, 08 Dec 2021 23:21:13: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 23:21:16: 13000000 INFO @ Wed, 08 Dec 2021 23:21:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180777/SRX3180777.05_peaks.xls INFO @ Wed, 08 Dec 2021 23:21:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180777/SRX3180777.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:21:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180777/SRX3180777.05_summits.bed INFO @ Wed, 08 Dec 2021 23:21:19: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (721 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 23:21:19: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 23:21:19: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 23:21:19: #1 total tags in treatment: 13345281 INFO @ Wed, 08 Dec 2021 23:21:19: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:21:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 23:21:19: #1 tags after filtering in treatment: 13345281 INFO @ Wed, 08 Dec 2021 23:21:19: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 23:21:19: #1 finished! INFO @ Wed, 08 Dec 2021 23:21:19: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:21:19: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:21:20: 9000000 INFO @ Wed, 08 Dec 2021 23:21:20: #2 number of paired peaks: 401 WARNING @ Wed, 08 Dec 2021 23:21:20: Fewer paired peaks (401) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 401 pairs to build model! INFO @ Wed, 08 Dec 2021 23:21:20: start model_add_line... INFO @ Wed, 08 Dec 2021 23:21:20: start X-correlation... INFO @ Wed, 08 Dec 2021 23:21:20: end of X-cor INFO @ Wed, 08 Dec 2021 23:21:20: #2 finished! INFO @ Wed, 08 Dec 2021 23:21:20: #2 predicted fragment length is 47 bps INFO @ Wed, 08 Dec 2021 23:21:20: #2 alternative fragment length(s) may be 2,47,531,547,576 bps INFO @ Wed, 08 Dec 2021 23:21:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180777/SRX3180777.10_model.r WARNING @ Wed, 08 Dec 2021 23:21:20: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 23:21:20: #2 You may need to consider one of the other alternative d(s): 2,47,531,547,576 WARNING @ Wed, 08 Dec 2021 23:21:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 23:21:20: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:21:20: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:21:26: 10000000 INFO @ Wed, 08 Dec 2021 23:21:32: 11000000 INFO @ Wed, 08 Dec 2021 23:21:37: 12000000 INFO @ Wed, 08 Dec 2021 23:21:43: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:21:43: 13000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 23:21:45: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 23:21:45: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 23:21:45: #1 total tags in treatment: 13345281 INFO @ Wed, 08 Dec 2021 23:21:45: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:21:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 23:21:46: #1 tags after filtering in treatment: 13345281 INFO @ Wed, 08 Dec 2021 23:21:46: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 23:21:46: #1 finished! INFO @ Wed, 08 Dec 2021 23:21:46: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:21:46: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:21:46: #2 number of paired peaks: 401 WARNING @ Wed, 08 Dec 2021 23:21:46: Fewer paired peaks (401) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 401 pairs to build model! INFO @ Wed, 08 Dec 2021 23:21:46: start model_add_line... INFO @ Wed, 08 Dec 2021 23:21:47: start X-correlation... INFO @ Wed, 08 Dec 2021 23:21:47: end of X-cor INFO @ Wed, 08 Dec 2021 23:21:47: #2 finished! INFO @ Wed, 08 Dec 2021 23:21:47: #2 predicted fragment length is 47 bps INFO @ Wed, 08 Dec 2021 23:21:47: #2 alternative fragment length(s) may be 2,47,531,547,576 bps INFO @ Wed, 08 Dec 2021 23:21:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180777/SRX3180777.20_model.r WARNING @ Wed, 08 Dec 2021 23:21:47: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 23:21:47: #2 You may need to consider one of the other alternative d(s): 2,47,531,547,576 WARNING @ Wed, 08 Dec 2021 23:21:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 23:21:47: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:21:47: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:21:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180777/SRX3180777.10_peaks.xls INFO @ Wed, 08 Dec 2021 23:21:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180777/SRX3180777.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:21:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180777/SRX3180777.10_summits.bed INFO @ Wed, 08 Dec 2021 23:21:55: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (478 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 23:22:10: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:22:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180777/SRX3180777.20_peaks.xls INFO @ Wed, 08 Dec 2021 23:22:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180777/SRX3180777.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:22:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180777/SRX3180777.20_summits.bed INFO @ Wed, 08 Dec 2021 23:22:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (199 records, 4 fields): 1 millis CompletedMACS2peakCalling