Job ID = 14159316 SRX = SRX8976727 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:10:44 14244035 reads; of these: 14244035 (100.00%) were paired; of these: 386860 (2.72%) aligned concordantly 0 times 12036762 (84.50%) aligned concordantly exactly 1 time 1820413 (12.78%) aligned concordantly >1 times ---- 386860 pairs aligned concordantly 0 times; of these: 227565 (58.82%) aligned discordantly 1 time ---- 159295 pairs aligned 0 times concordantly or discordantly; of these: 318590 mates make up the pairs; of these: 144775 (45.44%) aligned 0 times 90133 (28.29%) aligned exactly 1 time 83682 (26.27%) aligned >1 times 99.49% overall alignment rate Time searching: 00:10:44 Overall time: 00:10:44 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 12 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] 383673 / 14051394 = 0.0273 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 21:10:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976727/SRX8976727.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976727/SRX8976727.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976727/SRX8976727.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976727/SRX8976727.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 21:10:34: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:10:34: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:10:39: 1000000 INFO @ Wed, 08 Dec 2021 21:10:45: 2000000 INFO @ Wed, 08 Dec 2021 21:10:50: 3000000 INFO @ Wed, 08 Dec 2021 21:10:56: 4000000 INFO @ Wed, 08 Dec 2021 21:11:01: 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 21:11:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976727/SRX8976727.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976727/SRX8976727.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976727/SRX8976727.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976727/SRX8976727.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 21:11:04: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:11:04: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:11:07: 6000000 INFO @ Wed, 08 Dec 2021 21:11:10: 1000000 INFO @ Wed, 08 Dec 2021 21:11:13: 7000000 INFO @ Wed, 08 Dec 2021 21:11:15: 2000000 INFO @ Wed, 08 Dec 2021 21:11:18: 8000000 INFO @ Wed, 08 Dec 2021 21:11:21: 3000000 INFO @ Wed, 08 Dec 2021 21:11:24: 9000000 INFO @ Wed, 08 Dec 2021 21:11:26: 4000000 INFO @ Wed, 08 Dec 2021 21:11:30: 10000000 INFO @ Wed, 08 Dec 2021 21:11:32: 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 21:11:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976727/SRX8976727.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976727/SRX8976727.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976727/SRX8976727.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976727/SRX8976727.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 21:11:34: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:11:34: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:11:35: 11000000 INFO @ Wed, 08 Dec 2021 21:11:37: 6000000 INFO @ Wed, 08 Dec 2021 21:11:40: 1000000 INFO @ Wed, 08 Dec 2021 21:11:41: 12000000 INFO @ Wed, 08 Dec 2021 21:11:43: 7000000 INFO @ Wed, 08 Dec 2021 21:11:45: 2000000 INFO @ Wed, 08 Dec 2021 21:11:47: 13000000 INFO @ Wed, 08 Dec 2021 21:11:49: 8000000 INFO @ Wed, 08 Dec 2021 21:11:51: 3000000 INFO @ Wed, 08 Dec 2021 21:11:53: 14000000 INFO @ Wed, 08 Dec 2021 21:11:54: 9000000 INFO @ Wed, 08 Dec 2021 21:11:57: 4000000 INFO @ Wed, 08 Dec 2021 21:11:58: 15000000 INFO @ Wed, 08 Dec 2021 21:12:00: 10000000 INFO @ Wed, 08 Dec 2021 21:12:03: 5000000 INFO @ Wed, 08 Dec 2021 21:12:04: 16000000 INFO @ Wed, 08 Dec 2021 21:12:06: 11000000 INFO @ Wed, 08 Dec 2021 21:12:08: 6000000 INFO @ Wed, 08 Dec 2021 21:12:10: 17000000 INFO @ Wed, 08 Dec 2021 21:12:11: 12000000 INFO @ Wed, 08 Dec 2021 21:12:14: 7000000 INFO @ Wed, 08 Dec 2021 21:12:15: 18000000 INFO @ Wed, 08 Dec 2021 21:12:17: 13000000 INFO @ Wed, 08 Dec 2021 21:12:20: 8000000 INFO @ Wed, 08 Dec 2021 21:12:21: 19000000 INFO @ Wed, 08 Dec 2021 21:12:23: 14000000 INFO @ Wed, 08 Dec 2021 21:12:26: 9000000 INFO @ Wed, 08 Dec 2021 21:12:27: 20000000 INFO @ Wed, 08 Dec 2021 21:12:29: 15000000 INFO @ Wed, 08 Dec 2021 21:12:31: 10000000 INFO @ Wed, 08 Dec 2021 21:12:32: 21000000 INFO @ Wed, 08 Dec 2021 21:12:34: 16000000 INFO @ Wed, 08 Dec 2021 21:12:37: 11000000 INFO @ Wed, 08 Dec 2021 21:12:38: 22000000 INFO @ Wed, 08 Dec 2021 21:12:40: 17000000 INFO @ Wed, 08 Dec 2021 21:12:43: 12000000 INFO @ Wed, 08 Dec 2021 21:12:44: 23000000 INFO @ Wed, 08 Dec 2021 21:12:46: 18000000 INFO @ Wed, 08 Dec 2021 21:12:49: 13000000 INFO @ Wed, 08 Dec 2021 21:12:50: 24000000 INFO @ Wed, 08 Dec 2021 21:12:51: 19000000 INFO @ Wed, 08 Dec 2021 21:12:54: 14000000 INFO @ Wed, 08 Dec 2021 21:12:55: 25000000 INFO @ Wed, 08 Dec 2021 21:12:57: 20000000 INFO @ Wed, 08 Dec 2021 21:13:00: 15000000 INFO @ Wed, 08 Dec 2021 21:13:01: 26000000 INFO @ Wed, 08 Dec 2021 21:13:03: 21000000 INFO @ Wed, 08 Dec 2021 21:13:06: 16000000 INFO @ Wed, 08 Dec 2021 21:13:07: 27000000 INFO @ Wed, 08 Dec 2021 21:13:08: 22000000 INFO @ Wed, 08 Dec 2021 21:13:10: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 21:13:10: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 21:13:10: #1 total tags in treatment: 13477006 INFO @ Wed, 08 Dec 2021 21:13:10: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:13:10: #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 21:13:10: #1 tags after filtering in treatment: 12538081 INFO @ Wed, 08 Dec 2021 21:13:10: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 21:13:10: #1 finished! INFO @ Wed, 08 Dec 2021 21:13:10: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:13:10: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:13:11: #2 number of paired peaks: 331 WARNING @ Wed, 08 Dec 2021 21:13:11: Fewer paired peaks (331) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 331 pairs to build model! INFO @ Wed, 08 Dec 2021 21:13:11: start model_add_line... INFO @ Wed, 08 Dec 2021 21:13:11: start X-correlation... INFO @ Wed, 08 Dec 2021 21:13:11: end of X-cor INFO @ Wed, 08 Dec 2021 21:13:11: #2 finished! INFO @ Wed, 08 Dec 2021 21:13:11: #2 predicted fragment length is 175 bps INFO @ Wed, 08 Dec 2021 21:13:11: #2 alternative fragment length(s) may be 4,86,105,139,159,175 bps INFO @ Wed, 08 Dec 2021 21:13:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976727/SRX8976727.05_model.r INFO @ Wed, 08 Dec 2021 21:13:11: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:13:11: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:13:11: 17000000 INFO @ Wed, 08 Dec 2021 21:13:14: 23000000 INFO @ Wed, 08 Dec 2021 21:13:17: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 21:13:20: 24000000 INFO @ Wed, 08 Dec 2021 21:13:23: 19000000 INFO @ Wed, 08 Dec 2021 21:13:25: 25000000 INFO @ Wed, 08 Dec 2021 21:13:29: 20000000 INFO @ Wed, 08 Dec 2021 21:13:31: 26000000 INFO @ Wed, 08 Dec 2021 21:13:34: 21000000 INFO @ Wed, 08 Dec 2021 21:13:35: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:13:36: 27000000 INFO @ Wed, 08 Dec 2021 21:13:39: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 21:13:39: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 21:13:39: #1 total tags in treatment: 13477006 INFO @ Wed, 08 Dec 2021 21:13:39: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:13:39: #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 21:13:40: #1 tags after filtering in treatment: 12538081 INFO @ Wed, 08 Dec 2021 21:13:40: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 21:13:40: #1 finished! INFO @ Wed, 08 Dec 2021 21:13:40: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:13:40: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:13:40: 22000000 INFO @ Wed, 08 Dec 2021 21:13:41: #2 number of paired peaks: 331 WARNING @ Wed, 08 Dec 2021 21:13:41: Fewer paired peaks (331) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 331 pairs to build model! INFO @ Wed, 08 Dec 2021 21:13:41: start model_add_line... INFO @ Wed, 08 Dec 2021 21:13:41: start X-correlation... INFO @ Wed, 08 Dec 2021 21:13:41: end of X-cor INFO @ Wed, 08 Dec 2021 21:13:41: #2 finished! INFO @ Wed, 08 Dec 2021 21:13:41: #2 predicted fragment length is 175 bps INFO @ Wed, 08 Dec 2021 21:13:41: #2 alternative fragment length(s) may be 4,86,105,139,159,175 bps INFO @ Wed, 08 Dec 2021 21:13:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976727/SRX8976727.10_model.r INFO @ Wed, 08 Dec 2021 21:13:41: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:13:41: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:13:45: 23000000 INFO @ Wed, 08 Dec 2021 21:13:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976727/SRX8976727.05_peaks.xls INFO @ Wed, 08 Dec 2021 21:13:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976727/SRX8976727.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:13:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976727/SRX8976727.05_summits.bed INFO @ Wed, 08 Dec 2021 21:13:46: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (316 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 21:13:51: 24000000 INFO @ Wed, 08 Dec 2021 21:13:56: 25000000 INFO @ Wed, 08 Dec 2021 21:14:01: 26000000 INFO @ Wed, 08 Dec 2021 21:14:05: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:14:06: 27000000 INFO @ Wed, 08 Dec 2021 21:14:09: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 21:14:09: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 21:14:09: #1 total tags in treatment: 13477006 INFO @ Wed, 08 Dec 2021 21:14:09: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:14:09: #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 21:14:10: #1 tags after filtering in treatment: 12538081 INFO @ Wed, 08 Dec 2021 21:14:10: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 21:14:10: #1 finished! INFO @ Wed, 08 Dec 2021 21:14:10: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:14:10: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:14:10: #2 number of paired peaks: 331 WARNING @ Wed, 08 Dec 2021 21:14:10: Fewer paired peaks (331) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 331 pairs to build model! INFO @ Wed, 08 Dec 2021 21:14:10: start model_add_line... INFO @ Wed, 08 Dec 2021 21:14:11: start X-correlation... INFO @ Wed, 08 Dec 2021 21:14:11: end of X-cor INFO @ Wed, 08 Dec 2021 21:14:11: #2 finished! INFO @ Wed, 08 Dec 2021 21:14:11: #2 predicted fragment length is 175 bps INFO @ Wed, 08 Dec 2021 21:14:11: #2 alternative fragment length(s) may be 4,86,105,139,159,175 bps INFO @ Wed, 08 Dec 2021 21:14:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976727/SRX8976727.20_model.r INFO @ Wed, 08 Dec 2021 21:14:11: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:14:11: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 21:14:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976727/SRX8976727.10_peaks.xls INFO @ Wed, 08 Dec 2021 21:14:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976727/SRX8976727.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:14:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976727/SRX8976727.10_summits.bed INFO @ Wed, 08 Dec 2021 21:14:16: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (248 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 21:14:35: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:14:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976727/SRX8976727.20_peaks.xls INFO @ Wed, 08 Dec 2021 21:14:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976727/SRX8976727.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:14:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976727/SRX8976727.20_summits.bed INFO @ Wed, 08 Dec 2021 21:14:46: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (171 records, 4 fields): 3 millis CompletedMACS2peakCalling