Job ID = 14159557 SRX = SRX8845649 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 47129594 spots for SRR12345956/SRR12345956.sra Written 47129594 spots for SRR12345956/SRR12345956.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159954 ("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: 00:36:42 47129594 reads; of these: 47129594 (100.00%) were paired; of these: 20565034 (43.64%) aligned concordantly 0 times 22546478 (47.84%) aligned concordantly exactly 1 time 4018082 (8.53%) aligned concordantly >1 times ---- 20565034 pairs aligned concordantly 0 times; of these: 4850975 (23.59%) aligned discordantly 1 time ---- 15714059 pairs aligned 0 times concordantly or discordantly; of these: 31428118 mates make up the pairs; of these: 28852365 (91.80%) aligned 0 times 1256808 (4.00%) aligned exactly 1 time 1318945 (4.20%) aligned >1 times 69.39% overall alignment rate Time searching: 00:36:42 Overall time: 00:36:42 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 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] 23460869 / 31085109 = 0.7547 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 23:26:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845649/SRX8845649.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845649/SRX8845649.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845649/SRX8845649.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845649/SRX8845649.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 23:26:22: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:26:22: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:26:27: 1000000 INFO @ Wed, 08 Dec 2021 23:26:32: 2000000 INFO @ Wed, 08 Dec 2021 23:26:37: 3000000 INFO @ Wed, 08 Dec 2021 23:26:42: 4000000 INFO @ Wed, 08 Dec 2021 23:26:47: 5000000 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 23:26:52: 6000000 INFO @ Wed, 08 Dec 2021 23:26:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845649/SRX8845649.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845649/SRX8845649.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845649/SRX8845649.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845649/SRX8845649.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 23:26:52: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:26:52: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:26:57: 7000000 INFO @ Wed, 08 Dec 2021 23:26:57: 1000000 INFO @ Wed, 08 Dec 2021 23:27:03: 8000000 INFO @ Wed, 08 Dec 2021 23:27:03: 2000000 INFO @ Wed, 08 Dec 2021 23:27:08: 9000000 INFO @ Wed, 08 Dec 2021 23:27:09: 3000000 INFO @ Wed, 08 Dec 2021 23:27:14: 10000000 INFO @ Wed, 08 Dec 2021 23:27:14: 4000000 INFO @ Wed, 08 Dec 2021 23:27:20: 11000000 INFO @ Wed, 08 Dec 2021 23:27:20: 5000000 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 23:27:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845649/SRX8845649.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845649/SRX8845649.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845649/SRX8845649.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845649/SRX8845649.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 23:27:22: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:27:22: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:27:25: 12000000 INFO @ Wed, 08 Dec 2021 23:27:25: 6000000 INFO @ Wed, 08 Dec 2021 23:27:27: 1000000 INFO @ Wed, 08 Dec 2021 23:27:31: 13000000 INFO @ Wed, 08 Dec 2021 23:27:31: 7000000 INFO @ Wed, 08 Dec 2021 23:27:33: 2000000 INFO @ Wed, 08 Dec 2021 23:27:37: 14000000 INFO @ Wed, 08 Dec 2021 23:27:37: 8000000 INFO @ Wed, 08 Dec 2021 23:27:39: 3000000 INFO @ Wed, 08 Dec 2021 23:27:42: 15000000 INFO @ Wed, 08 Dec 2021 23:27:42: 9000000 INFO @ Wed, 08 Dec 2021 23:27:44: 4000000 INFO @ Wed, 08 Dec 2021 23:27:48: 16000000 INFO @ Wed, 08 Dec 2021 23:27:48: 10000000 INFO @ Wed, 08 Dec 2021 23:27:50: 5000000 INFO @ Wed, 08 Dec 2021 23:27:53: 17000000 INFO @ Wed, 08 Dec 2021 23:27:54: 11000000 INFO @ Wed, 08 Dec 2021 23:27:55: 6000000 INFO @ Wed, 08 Dec 2021 23:27:59: 18000000 INFO @ Wed, 08 Dec 2021 23:27:59: 12000000 INFO @ Wed, 08 Dec 2021 23:28:01: 7000000 INFO @ Wed, 08 Dec 2021 23:28:02: #1 tag size is determined as 73 bps INFO @ Wed, 08 Dec 2021 23:28:02: #1 tag size = 73 INFO @ Wed, 08 Dec 2021 23:28:02: #1 total tags in treatment: 6186362 INFO @ Wed, 08 Dec 2021 23:28:02: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:28:02: #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 23:28:02: #1 tags after filtering in treatment: 4760315 INFO @ Wed, 08 Dec 2021 23:28:02: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 08 Dec 2021 23:28:02: #1 finished! INFO @ Wed, 08 Dec 2021 23:28:02: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:28:02: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:28:02: #2 number of paired peaks: 783 WARNING @ Wed, 08 Dec 2021 23:28:02: Fewer paired peaks (783) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 783 pairs to build model! INFO @ Wed, 08 Dec 2021 23:28:02: start model_add_line... INFO @ Wed, 08 Dec 2021 23:28:02: start X-correlation... INFO @ Wed, 08 Dec 2021 23:28:02: end of X-cor INFO @ Wed, 08 Dec 2021 23:28:02: #2 finished! INFO @ Wed, 08 Dec 2021 23:28:02: #2 predicted fragment length is 116 bps INFO @ Wed, 08 Dec 2021 23:28:02: #2 alternative fragment length(s) may be 116 bps INFO @ Wed, 08 Dec 2021 23:28:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845649/SRX8845649.05_model.r WARNING @ Wed, 08 Dec 2021 23:28:02: #2 Since the d (116) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 23:28:02: #2 You may need to consider one of the other alternative d(s): 116 WARNING @ Wed, 08 Dec 2021 23:28:02: #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 23:28:02: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:28:02: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:28:05: 13000000 INFO @ Wed, 08 Dec 2021 23:28:07: 8000000 INFO @ Wed, 08 Dec 2021 23:28:10: 14000000 INFO @ Wed, 08 Dec 2021 23:28:12: 9000000 INFO @ Wed, 08 Dec 2021 23:28:12: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:28:16: 15000000 INFO @ Wed, 08 Dec 2021 23:28:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845649/SRX8845649.05_peaks.xls INFO @ Wed, 08 Dec 2021 23:28:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845649/SRX8845649.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:28:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845649/SRX8845649.05_summits.bed INFO @ Wed, 08 Dec 2021 23:28:17: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1946 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 23:28:18: 10000000 INFO @ Wed, 08 Dec 2021 23:28:21: 16000000 INFO @ Wed, 08 Dec 2021 23:28:23: 11000000 INFO @ Wed, 08 Dec 2021 23:28:27: 17000000 INFO @ Wed, 08 Dec 2021 23:28:29: 12000000 INFO @ Wed, 08 Dec 2021 23:28:33: 18000000 INFO @ Wed, 08 Dec 2021 23:28:34: 13000000 INFO @ Wed, 08 Dec 2021 23:28:36: #1 tag size is determined as 73 bps INFO @ Wed, 08 Dec 2021 23:28:36: #1 tag size = 73 INFO @ Wed, 08 Dec 2021 23:28:36: #1 total tags in treatment: 6186362 INFO @ Wed, 08 Dec 2021 23:28:36: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:28:36: #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 23:28:36: #1 tags after filtering in treatment: 4760315 INFO @ Wed, 08 Dec 2021 23:28:36: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 08 Dec 2021 23:28:36: #1 finished! INFO @ Wed, 08 Dec 2021 23:28:36: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:28:36: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:28:36: #2 number of paired peaks: 783 WARNING @ Wed, 08 Dec 2021 23:28:36: Fewer paired peaks (783) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 783 pairs to build model! INFO @ Wed, 08 Dec 2021 23:28:36: start model_add_line... INFO @ Wed, 08 Dec 2021 23:28:36: start X-correlation... INFO @ Wed, 08 Dec 2021 23:28:36: end of X-cor INFO @ Wed, 08 Dec 2021 23:28:36: #2 finished! INFO @ Wed, 08 Dec 2021 23:28:36: #2 predicted fragment length is 116 bps INFO @ Wed, 08 Dec 2021 23:28:36: #2 alternative fragment length(s) may be 116 bps INFO @ Wed, 08 Dec 2021 23:28:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845649/SRX8845649.10_model.r WARNING @ Wed, 08 Dec 2021 23:28:36: #2 Since the d (116) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 23:28:36: #2 You may need to consider one of the other alternative d(s): 116 WARNING @ Wed, 08 Dec 2021 23:28:36: #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 23:28:36: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:28:36: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 23:28:40: 14000000 INFO @ Wed, 08 Dec 2021 23:28:45: 15000000 INFO @ Wed, 08 Dec 2021 23:28:47: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:28:50: 16000000 INFO @ Wed, 08 Dec 2021 23:28:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845649/SRX8845649.10_peaks.xls INFO @ Wed, 08 Dec 2021 23:28:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845649/SRX8845649.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:28:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845649/SRX8845649.10_summits.bed INFO @ Wed, 08 Dec 2021 23:28:52: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (980 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 23:28:56: 17000000 INFO @ Wed, 08 Dec 2021 23:29:01: 18000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 23:29:04: #1 tag size is determined as 73 bps INFO @ Wed, 08 Dec 2021 23:29:04: #1 tag size = 73 INFO @ Wed, 08 Dec 2021 23:29:04: #1 total tags in treatment: 6186362 INFO @ Wed, 08 Dec 2021 23:29:04: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:29:04: #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 23:29:04: #1 tags after filtering in treatment: 4760315 INFO @ Wed, 08 Dec 2021 23:29:04: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 08 Dec 2021 23:29:04: #1 finished! INFO @ Wed, 08 Dec 2021 23:29:04: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:29:04: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:29:04: #2 number of paired peaks: 783 WARNING @ Wed, 08 Dec 2021 23:29:04: Fewer paired peaks (783) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 783 pairs to build model! INFO @ Wed, 08 Dec 2021 23:29:04: start model_add_line... INFO @ Wed, 08 Dec 2021 23:29:04: start X-correlation... INFO @ Wed, 08 Dec 2021 23:29:04: end of X-cor INFO @ Wed, 08 Dec 2021 23:29:04: #2 finished! INFO @ Wed, 08 Dec 2021 23:29:04: #2 predicted fragment length is 116 bps INFO @ Wed, 08 Dec 2021 23:29:04: #2 alternative fragment length(s) may be 116 bps INFO @ Wed, 08 Dec 2021 23:29:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845649/SRX8845649.20_model.r WARNING @ Wed, 08 Dec 2021 23:29:04: #2 Since the d (116) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 23:29:04: #2 You may need to consider one of the other alternative d(s): 116 WARNING @ Wed, 08 Dec 2021 23:29:04: #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 23:29:04: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:29:04: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:29:15: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:29:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845649/SRX8845649.20_peaks.xls INFO @ Wed, 08 Dec 2021 23:29:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845649/SRX8845649.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:29:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845649/SRX8845649.20_summits.bed INFO @ Wed, 08 Dec 2021 23:29:20: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (327 records, 4 fields): 22 millis CompletedMACS2peakCalling