Job ID = 12264813 SRX = SRX7246270 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 9787133 spots for SRR10564684/SRR10564684.sra Written 9787133 spots for SRR10564684/SRR10564684.sra Read 9940298 spots for SRR10564685/SRR10564685.sra Written 9940298 spots for SRR10564685/SRR10564685.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265428 ("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: 00:37:35 19727431 reads; of these: 19727431 (100.00%) were paired; of these: 923130 (4.68%) aligned concordantly 0 times 15327922 (77.70%) aligned concordantly exactly 1 time 3476379 (17.62%) aligned concordantly >1 times ---- 923130 pairs aligned concordantly 0 times; of these: 250510 (27.14%) aligned discordantly 1 time ---- 672620 pairs aligned 0 times concordantly or discordantly; of these: 1345240 mates make up the pairs; of these: 919192 (68.33%) aligned 0 times 264463 (19.66%) aligned exactly 1 time 161585 (12.01%) aligned >1 times 97.67% overall alignment rate Time searching: 00:37:35 Overall time: 00:37:35 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 16 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] 3037320 / 12485315 = 0.2433 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:57:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7246270/SRX7246270.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7246270/SRX7246270.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7246270/SRX7246270.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7246270/SRX7246270.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 @ Sat, 03 Apr 2021 06:57:20: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:57:20: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:57:27: 1000000 INFO @ Sat, 03 Apr 2021 06:57:34: 2000000 INFO @ Sat, 03 Apr 2021 06:57:42: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:57:49: 4000000 INFO @ Sat, 03 Apr 2021 06:57:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7246270/SRX7246270.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7246270/SRX7246270.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7246270/SRX7246270.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7246270/SRX7246270.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 @ Sat, 03 Apr 2021 06:57:50: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:57:50: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:57:56: 5000000 INFO @ Sat, 03 Apr 2021 06:57:59: 1000000 INFO @ Sat, 03 Apr 2021 06:58:03: 6000000 INFO @ Sat, 03 Apr 2021 06:58:09: 2000000 INFO @ Sat, 03 Apr 2021 06:58:10: 7000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:58:18: 8000000 INFO @ Sat, 03 Apr 2021 06:58:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7246270/SRX7246270.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7246270/SRX7246270.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7246270/SRX7246270.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7246270/SRX7246270.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 @ Sat, 03 Apr 2021 06:58:20: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:58:20: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:58:21: 3000000 INFO @ Sat, 03 Apr 2021 06:58:27: 9000000 INFO @ Sat, 03 Apr 2021 06:58:32: 1000000 INFO @ Sat, 03 Apr 2021 06:58:32: 4000000 INFO @ Sat, 03 Apr 2021 06:58:37: 10000000 INFO @ Sat, 03 Apr 2021 06:58:44: 5000000 INFO @ Sat, 03 Apr 2021 06:58:44: 2000000 INFO @ Sat, 03 Apr 2021 06:58:47: 11000000 INFO @ Sat, 03 Apr 2021 06:58:53: 6000000 INFO @ Sat, 03 Apr 2021 06:58:55: 3000000 INFO @ Sat, 03 Apr 2021 06:58:58: 12000000 INFO @ Sat, 03 Apr 2021 06:59:04: 7000000 INFO @ Sat, 03 Apr 2021 06:59:06: 4000000 INFO @ Sat, 03 Apr 2021 06:59:08: 13000000 INFO @ Sat, 03 Apr 2021 06:59:14: 8000000 INFO @ Sat, 03 Apr 2021 06:59:16: 5000000 INFO @ Sat, 03 Apr 2021 06:59:18: 14000000 INFO @ Sat, 03 Apr 2021 06:59:24: 9000000 INFO @ Sat, 03 Apr 2021 06:59:26: 6000000 INFO @ Sat, 03 Apr 2021 06:59:28: 15000000 INFO @ Sat, 03 Apr 2021 06:59:36: 10000000 INFO @ Sat, 03 Apr 2021 06:59:36: 7000000 INFO @ Sat, 03 Apr 2021 06:59:38: 16000000 INFO @ Sat, 03 Apr 2021 06:59:46: 11000000 INFO @ Sat, 03 Apr 2021 06:59:46: 8000000 INFO @ Sat, 03 Apr 2021 06:59:49: 17000000 INFO @ Sat, 03 Apr 2021 06:59:55: 12000000 INFO @ Sat, 03 Apr 2021 06:59:56: 9000000 INFO @ Sat, 03 Apr 2021 06:59:59: 18000000 INFO @ Sat, 03 Apr 2021 07:00:06: 13000000 INFO @ Sat, 03 Apr 2021 07:00:06: 10000000 INFO @ Sat, 03 Apr 2021 07:00:08: 19000000 INFO @ Sat, 03 Apr 2021 07:00:16: 11000000 INFO @ Sat, 03 Apr 2021 07:00:17: 14000000 INFO @ Sat, 03 Apr 2021 07:00:18: 20000000 INFO @ Sat, 03 Apr 2021 07:00:25: 12000000 INFO @ Sat, 03 Apr 2021 07:00:27: 21000000 INFO @ Sat, 03 Apr 2021 07:00:27: 15000000 INFO @ Sat, 03 Apr 2021 07:00:34: 13000000 INFO @ Sat, 03 Apr 2021 07:00:36: 22000000 INFO @ Sat, 03 Apr 2021 07:00:38: 16000000 INFO @ Sat, 03 Apr 2021 07:00:43: 14000000 INFO @ Sat, 03 Apr 2021 07:00:45: 23000000 INFO @ Sat, 03 Apr 2021 07:00:48: 17000000 INFO @ Sat, 03 Apr 2021 07:00:52: 15000000 INFO @ Sat, 03 Apr 2021 07:00:53: 24000000 INFO @ Sat, 03 Apr 2021 07:00:58: 18000000 INFO @ Sat, 03 Apr 2021 07:01:00: 16000000 INFO @ Sat, 03 Apr 2021 07:01:02: 25000000 INFO @ Sat, 03 Apr 2021 07:01:08: 19000000 INFO @ Sat, 03 Apr 2021 07:01:09: 17000000 INFO @ Sat, 03 Apr 2021 07:01:11: 26000000 INFO @ Sat, 03 Apr 2021 07:01:18: 18000000 INFO @ Sat, 03 Apr 2021 07:01:19: 20000000 INFO @ Sat, 03 Apr 2021 07:01:20: 27000000 INFO @ Sat, 03 Apr 2021 07:01:26: 19000000 INFO @ Sat, 03 Apr 2021 07:01:30: 28000000 INFO @ Sat, 03 Apr 2021 07:01:30: 21000000 INFO @ Sat, 03 Apr 2021 07:01:35: 20000000 INFO @ Sat, 03 Apr 2021 07:01:40: 29000000 INFO @ Sat, 03 Apr 2021 07:01:42: 22000000 INFO @ Sat, 03 Apr 2021 07:01:45: 21000000 INFO @ Sat, 03 Apr 2021 07:01:49: 30000000 INFO @ Sat, 03 Apr 2021 07:01:54: 22000000 INFO @ Sat, 03 Apr 2021 07:01:54: 23000000 INFO @ Sat, 03 Apr 2021 07:01:57: 31000000 INFO @ Sat, 03 Apr 2021 07:02:02: 23000000 INFO @ Sat, 03 Apr 2021 07:02:05: 32000000 INFO @ Sat, 03 Apr 2021 07:02:05: 24000000 INFO @ Sat, 03 Apr 2021 07:02:09: #1 tag size is determined as 92 bps INFO @ Sat, 03 Apr 2021 07:02:09: #1 tag size = 92 INFO @ Sat, 03 Apr 2021 07:02:09: #1 total tags in treatment: 15771780 INFO @ Sat, 03 Apr 2021 07:02:09: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:02:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:02:10: #1 tags after filtering in treatment: 10716994 INFO @ Sat, 03 Apr 2021 07:02:10: #1 Redundant rate of treatment: 0.32 INFO @ Sat, 03 Apr 2021 07:02:10: #1 finished! INFO @ Sat, 03 Apr 2021 07:02:10: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:02:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:02:10: 24000000 INFO @ Sat, 03 Apr 2021 07:02:10: #2 number of paired peaks: 307 WARNING @ Sat, 03 Apr 2021 07:02:10: Fewer paired peaks (307) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 307 pairs to build model! INFO @ Sat, 03 Apr 2021 07:02:10: start model_add_line... INFO @ Sat, 03 Apr 2021 07:02:10: start X-correlation... INFO @ Sat, 03 Apr 2021 07:02:11: end of X-cor INFO @ Sat, 03 Apr 2021 07:02:11: #2 finished! INFO @ Sat, 03 Apr 2021 07:02:11: #2 predicted fragment length is 99 bps INFO @ Sat, 03 Apr 2021 07:02:11: #2 alternative fragment length(s) may be 99,107,598 bps INFO @ Sat, 03 Apr 2021 07:02:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7246270/SRX7246270.05_model.r WARNING @ Sat, 03 Apr 2021 07:02:11: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:02:11: #2 You may need to consider one of the other alternative d(s): 99,107,598 WARNING @ Sat, 03 Apr 2021 07:02:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:02:11: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:02:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:02:16: 25000000 INFO @ Sat, 03 Apr 2021 07:02:18: 25000000 INFO @ Sat, 03 Apr 2021 07:02:27: 26000000 INFO @ Sat, 03 Apr 2021 07:02:29: 26000000 INFO @ Sat, 03 Apr 2021 07:02:32: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:02:37: 27000000 INFO @ Sat, 03 Apr 2021 07:02:37: 27000000 INFO @ Sat, 03 Apr 2021 07:02:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7246270/SRX7246270.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:02:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7246270/SRX7246270.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:02:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7246270/SRX7246270.05_summits.bed INFO @ Sat, 03 Apr 2021 07:02:43: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3711 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:02:44: 28000000 INFO @ Sat, 03 Apr 2021 07:02:47: 28000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:02:52: 29000000 INFO @ Sat, 03 Apr 2021 07:02:58: 29000000 INFO @ Sat, 03 Apr 2021 07:02:58: 30000000 INFO @ Sat, 03 Apr 2021 07:03:05: 31000000 INFO @ Sat, 03 Apr 2021 07:03:08: 30000000 INFO @ Sat, 03 Apr 2021 07:03:12: 32000000 INFO @ Sat, 03 Apr 2021 07:03:15: 31000000 INFO @ Sat, 03 Apr 2021 07:03:16: #1 tag size is determined as 92 bps INFO @ Sat, 03 Apr 2021 07:03:16: #1 tag size = 92 INFO @ Sat, 03 Apr 2021 07:03:16: #1 total tags in treatment: 15771780 INFO @ Sat, 03 Apr 2021 07:03:16: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:03:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:03:16: #1 tags after filtering in treatment: 10716994 INFO @ Sat, 03 Apr 2021 07:03:16: #1 Redundant rate of treatment: 0.32 INFO @ Sat, 03 Apr 2021 07:03:16: #1 finished! INFO @ Sat, 03 Apr 2021 07:03:16: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:03:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:03:17: #2 number of paired peaks: 307 WARNING @ Sat, 03 Apr 2021 07:03:17: Fewer paired peaks (307) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 307 pairs to build model! INFO @ Sat, 03 Apr 2021 07:03:17: start model_add_line... INFO @ Sat, 03 Apr 2021 07:03:17: start X-correlation... INFO @ Sat, 03 Apr 2021 07:03:17: end of X-cor INFO @ Sat, 03 Apr 2021 07:03:17: #2 finished! INFO @ Sat, 03 Apr 2021 07:03:17: #2 predicted fragment length is 99 bps INFO @ Sat, 03 Apr 2021 07:03:17: #2 alternative fragment length(s) may be 99,107,598 bps INFO @ Sat, 03 Apr 2021 07:03:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7246270/SRX7246270.20_model.r WARNING @ Sat, 03 Apr 2021 07:03:17: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:03:17: #2 You may need to consider one of the other alternative d(s): 99,107,598 WARNING @ Sat, 03 Apr 2021 07:03:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:03:17: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:03:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:03:22: 32000000 INFO @ Sat, 03 Apr 2021 07:03:25: #1 tag size is determined as 92 bps INFO @ Sat, 03 Apr 2021 07:03:25: #1 tag size = 92 INFO @ Sat, 03 Apr 2021 07:03:25: #1 total tags in treatment: 15771780 INFO @ Sat, 03 Apr 2021 07:03:25: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:03:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:03:26: #1 tags after filtering in treatment: 10716994 INFO @ Sat, 03 Apr 2021 07:03:26: #1 Redundant rate of treatment: 0.32 INFO @ Sat, 03 Apr 2021 07:03:26: #1 finished! INFO @ Sat, 03 Apr 2021 07:03:26: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:03:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:03:26: #2 number of paired peaks: 307 WARNING @ Sat, 03 Apr 2021 07:03:26: Fewer paired peaks (307) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 307 pairs to build model! INFO @ Sat, 03 Apr 2021 07:03:26: start model_add_line... INFO @ Sat, 03 Apr 2021 07:03:26: start X-correlation... INFO @ Sat, 03 Apr 2021 07:03:26: end of X-cor INFO @ Sat, 03 Apr 2021 07:03:26: #2 finished! INFO @ Sat, 03 Apr 2021 07:03:26: #2 predicted fragment length is 99 bps INFO @ Sat, 03 Apr 2021 07:03:26: #2 alternative fragment length(s) may be 99,107,598 bps INFO @ Sat, 03 Apr 2021 07:03:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7246270/SRX7246270.10_model.r WARNING @ Sat, 03 Apr 2021 07:03:26: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:03:26: #2 You may need to consider one of the other alternative d(s): 99,107,598 WARNING @ Sat, 03 Apr 2021 07:03:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:03:26: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:03:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:03:37: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:03:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7246270/SRX7246270.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:03:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7246270/SRX7246270.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:03:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7246270/SRX7246270.20_summits.bed INFO @ Sat, 03 Apr 2021 07:03:48: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (870 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:03:48: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:03:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7246270/SRX7246270.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:03:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7246270/SRX7246270.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:03:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7246270/SRX7246270.10_summits.bed INFO @ Sat, 03 Apr 2021 07:03:59: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2091 records, 4 fields): 4 millis CompletedMACS2peakCalling