Job ID = 14159086 SRX = SRX8976733 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 13369914 spots for SRR12483277/SRR12483277.sra Written 13369914 spots for SRR12483277/SRR12483277.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159338 ("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: 00:10:24 13369914 reads; of these: 13369914 (100.00%) were paired; of these: 975105 (7.29%) aligned concordantly 0 times 10785385 (80.67%) aligned concordantly exactly 1 time 1609424 (12.04%) aligned concordantly >1 times ---- 975105 pairs aligned concordantly 0 times; of these: 724556 (74.31%) aligned discordantly 1 time ---- 250549 pairs aligned 0 times concordantly or discordantly; of these: 501098 mates make up the pairs; of these: 136308 (27.20%) aligned 0 times 160728 (32.08%) aligned exactly 1 time 204062 (40.72%) aligned >1 times 99.49% overall alignment rate Time searching: 00:10:24 Overall time: 00:10:24 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_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] 362967 / 13081900 = 0.0277 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 19:25:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976733/SRX8976733.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976733/SRX8976733.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976733/SRX8976733.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976733/SRX8976733.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 19:25:10: #1 read tag files... INFO @ Wed, 08 Dec 2021 19:25:10: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 19:25:15: 1000000 INFO @ Wed, 08 Dec 2021 19:25:20: 2000000 INFO @ Wed, 08 Dec 2021 19:25:25: 3000000 INFO @ Wed, 08 Dec 2021 19:25:30: 4000000 INFO @ Wed, 08 Dec 2021 19:25:35: 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 19:25:39: 6000000 INFO @ Wed, 08 Dec 2021 19:25:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976733/SRX8976733.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976733/SRX8976733.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976733/SRX8976733.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976733/SRX8976733.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 19:25:40: #1 read tag files... INFO @ Wed, 08 Dec 2021 19:25:40: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 19:25:45: 7000000 INFO @ Wed, 08 Dec 2021 19:25:46: 1000000 INFO @ Wed, 08 Dec 2021 19:25:51: 8000000 INFO @ Wed, 08 Dec 2021 19:25:53: 2000000 INFO @ Wed, 08 Dec 2021 19:25:56: 9000000 INFO @ Wed, 08 Dec 2021 19:25:59: 3000000 INFO @ Wed, 08 Dec 2021 19:26:02: 10000000 INFO @ Wed, 08 Dec 2021 19:26:05: 4000000 INFO @ Wed, 08 Dec 2021 19:26:08: 11000000 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 19:26:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976733/SRX8976733.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976733/SRX8976733.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976733/SRX8976733.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976733/SRX8976733.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 19:26:10: #1 read tag files... INFO @ Wed, 08 Dec 2021 19:26:10: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 19:26:12: 5000000 INFO @ Wed, 08 Dec 2021 19:26:14: 12000000 INFO @ Wed, 08 Dec 2021 19:26:17: 1000000 INFO @ Wed, 08 Dec 2021 19:26:18: 6000000 INFO @ Wed, 08 Dec 2021 19:26:20: 13000000 INFO @ Wed, 08 Dec 2021 19:26:23: 2000000 INFO @ Wed, 08 Dec 2021 19:26:25: 7000000 INFO @ Wed, 08 Dec 2021 19:26:25: 14000000 INFO @ Wed, 08 Dec 2021 19:26:30: 3000000 INFO @ Wed, 08 Dec 2021 19:26:31: 15000000 INFO @ Wed, 08 Dec 2021 19:26:31: 8000000 INFO @ Wed, 08 Dec 2021 19:26:36: 4000000 INFO @ Wed, 08 Dec 2021 19:26:37: 16000000 INFO @ Wed, 08 Dec 2021 19:26:38: 9000000 INFO @ Wed, 08 Dec 2021 19:26:43: 17000000 INFO @ Wed, 08 Dec 2021 19:26:43: 5000000 INFO @ Wed, 08 Dec 2021 19:26:44: 10000000 INFO @ Wed, 08 Dec 2021 19:26:48: 18000000 INFO @ Wed, 08 Dec 2021 19:26:49: 6000000 INFO @ Wed, 08 Dec 2021 19:26:51: 11000000 INFO @ Wed, 08 Dec 2021 19:26:54: 19000000 INFO @ Wed, 08 Dec 2021 19:26:55: 7000000 INFO @ Wed, 08 Dec 2021 19:26:57: 12000000 INFO @ Wed, 08 Dec 2021 19:26:59: 20000000 INFO @ Wed, 08 Dec 2021 19:27:02: 8000000 INFO @ Wed, 08 Dec 2021 19:27:04: 13000000 INFO @ Wed, 08 Dec 2021 19:27:05: 21000000 INFO @ Wed, 08 Dec 2021 19:27:09: 9000000 INFO @ Wed, 08 Dec 2021 19:27:10: 14000000 INFO @ Wed, 08 Dec 2021 19:27:11: 22000000 INFO @ Wed, 08 Dec 2021 19:27:15: 10000000 INFO @ Wed, 08 Dec 2021 19:27:17: 23000000 INFO @ Wed, 08 Dec 2021 19:27:17: 15000000 INFO @ Wed, 08 Dec 2021 19:27:21: 11000000 INFO @ Wed, 08 Dec 2021 19:27:22: 24000000 INFO @ Wed, 08 Dec 2021 19:27:23: 16000000 INFO @ Wed, 08 Dec 2021 19:27:28: 12000000 INFO @ Wed, 08 Dec 2021 19:27:28: 25000000 INFO @ Wed, 08 Dec 2021 19:27:30: 17000000 INFO @ Wed, 08 Dec 2021 19:27:33: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 19:27:33: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 19:27:33: #1 total tags in treatment: 12046808 INFO @ Wed, 08 Dec 2021 19:27:33: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 19:27:33: #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 19:27:33: #1 tags after filtering in treatment: 11298229 INFO @ Wed, 08 Dec 2021 19:27:33: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 19:27:33: #1 finished! INFO @ Wed, 08 Dec 2021 19:27:33: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 19:27:33: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 19:27:34: #2 number of paired peaks: 352 WARNING @ Wed, 08 Dec 2021 19:27:34: Fewer paired peaks (352) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 352 pairs to build model! INFO @ Wed, 08 Dec 2021 19:27:34: start model_add_line... INFO @ Wed, 08 Dec 2021 19:27:34: start X-correlation... INFO @ Wed, 08 Dec 2021 19:27:34: end of X-cor INFO @ Wed, 08 Dec 2021 19:27:34: #2 finished! INFO @ Wed, 08 Dec 2021 19:27:34: #2 predicted fragment length is 143 bps INFO @ Wed, 08 Dec 2021 19:27:34: #2 alternative fragment length(s) may be 4,143,153 bps INFO @ Wed, 08 Dec 2021 19:27:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976733/SRX8976733.05_model.r INFO @ Wed, 08 Dec 2021 19:27:34: #3 Call peaks... INFO @ Wed, 08 Dec 2021 19:27:34: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 19:27:34: 13000000 INFO @ Wed, 08 Dec 2021 19:27:36: 18000000 INFO @ Wed, 08 Dec 2021 19:27:40: 14000000 INFO @ Wed, 08 Dec 2021 19:27:42: 19000000 INFO @ Wed, 08 Dec 2021 19:27:46: 15000000 INFO @ Wed, 08 Dec 2021 19:27:48: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 19:27:52: 16000000 INFO @ Wed, 08 Dec 2021 19:27:54: 21000000 INFO @ Wed, 08 Dec 2021 19:27:57: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 19:27:59: 17000000 INFO @ Wed, 08 Dec 2021 19:28:00: 22000000 INFO @ Wed, 08 Dec 2021 19:28:05: 18000000 INFO @ Wed, 08 Dec 2021 19:28:06: 23000000 INFO @ Wed, 08 Dec 2021 19:28:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976733/SRX8976733.05_peaks.xls INFO @ Wed, 08 Dec 2021 19:28:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976733/SRX8976733.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 19:28:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976733/SRX8976733.05_summits.bed INFO @ Wed, 08 Dec 2021 19:28:08: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (345 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 19:28:11: 19000000 INFO @ Wed, 08 Dec 2021 19:28:12: 24000000 INFO @ Wed, 08 Dec 2021 19:28:17: 20000000 INFO @ Wed, 08 Dec 2021 19:28:18: 25000000 INFO @ Wed, 08 Dec 2021 19:28:23: 21000000 INFO @ Wed, 08 Dec 2021 19:28:23: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 19:28:23: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 19:28:23: #1 total tags in treatment: 12046808 INFO @ Wed, 08 Dec 2021 19:28:23: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 19:28:23: #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 19:28:23: #1 tags after filtering in treatment: 11298229 INFO @ Wed, 08 Dec 2021 19:28:23: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 19:28:23: #1 finished! INFO @ Wed, 08 Dec 2021 19:28:23: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 19:28:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 19:28:24: #2 number of paired peaks: 352 WARNING @ Wed, 08 Dec 2021 19:28:24: Fewer paired peaks (352) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 352 pairs to build model! INFO @ Wed, 08 Dec 2021 19:28:24: start model_add_line... INFO @ Wed, 08 Dec 2021 19:28:24: start X-correlation... INFO @ Wed, 08 Dec 2021 19:28:24: end of X-cor INFO @ Wed, 08 Dec 2021 19:28:24: #2 finished! INFO @ Wed, 08 Dec 2021 19:28:24: #2 predicted fragment length is 143 bps INFO @ Wed, 08 Dec 2021 19:28:24: #2 alternative fragment length(s) may be 4,143,153 bps INFO @ Wed, 08 Dec 2021 19:28:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976733/SRX8976733.10_model.r INFO @ Wed, 08 Dec 2021 19:28:24: #3 Call peaks... INFO @ Wed, 08 Dec 2021 19:28:24: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 19:28:28: 22000000 INFO @ Wed, 08 Dec 2021 19:28:34: 23000000 INFO @ Wed, 08 Dec 2021 19:28:40: 24000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 19:28:45: 25000000 INFO @ Wed, 08 Dec 2021 19:28:46: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 19:28:50: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 19:28:50: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 19:28:50: #1 total tags in treatment: 12046808 INFO @ Wed, 08 Dec 2021 19:28:50: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 19:28:50: #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 19:28:51: #1 tags after filtering in treatment: 11298229 INFO @ Wed, 08 Dec 2021 19:28:51: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 19:28:51: #1 finished! INFO @ Wed, 08 Dec 2021 19:28:51: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 19:28:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 19:28:51: #2 number of paired peaks: 352 WARNING @ Wed, 08 Dec 2021 19:28:51: Fewer paired peaks (352) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 352 pairs to build model! INFO @ Wed, 08 Dec 2021 19:28:51: start model_add_line... INFO @ Wed, 08 Dec 2021 19:28:51: start X-correlation... INFO @ Wed, 08 Dec 2021 19:28:51: end of X-cor INFO @ Wed, 08 Dec 2021 19:28:51: #2 finished! INFO @ Wed, 08 Dec 2021 19:28:51: #2 predicted fragment length is 143 bps INFO @ Wed, 08 Dec 2021 19:28:51: #2 alternative fragment length(s) may be 4,143,153 bps INFO @ Wed, 08 Dec 2021 19:28:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976733/SRX8976733.20_model.r INFO @ Wed, 08 Dec 2021 19:28:51: #3 Call peaks... INFO @ Wed, 08 Dec 2021 19:28:51: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 19:28:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976733/SRX8976733.10_peaks.xls INFO @ Wed, 08 Dec 2021 19:28:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976733/SRX8976733.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 19:28:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976733/SRX8976733.10_summits.bed INFO @ Wed, 08 Dec 2021 19:28:56: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (240 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 19:29:13: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 19:29:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976733/SRX8976733.20_peaks.xls INFO @ Wed, 08 Dec 2021 19:29:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976733/SRX8976733.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 19:29:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976733/SRX8976733.20_summits.bed INFO @ Wed, 08 Dec 2021 19:29:23: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (174 records, 4 fields): 2 millis CompletedMACS2peakCalling