Job ID = 14159206 SRX = SRX8976708 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: 00:10:27 10920239 reads; of these: 10920239 (100.00%) were paired; of these: 1990352 (18.23%) aligned concordantly 0 times 7009771 (64.19%) aligned concordantly exactly 1 time 1920116 (17.58%) aligned concordantly >1 times ---- 1990352 pairs aligned concordantly 0 times; of these: 1306117 (65.62%) aligned discordantly 1 time ---- 684235 pairs aligned 0 times concordantly or discordantly; of these: 1368470 mates make up the pairs; of these: 501015 (36.61%) aligned 0 times 342348 (25.02%) aligned exactly 1 time 525107 (38.37%) aligned >1 times 97.71% overall alignment rate Time searching: 00:10:27 Overall time: 00:10:27 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] 3172438 / 10230773 = 0.3101 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 20:26:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976708/SRX8976708.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976708/SRX8976708.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976708/SRX8976708.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976708/SRX8976708.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 20:26:32: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:26:32: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:26:36: 1000000 INFO @ Wed, 08 Dec 2021 20:26:40: 2000000 INFO @ Wed, 08 Dec 2021 20:26:44: 3000000 INFO @ Wed, 08 Dec 2021 20:26:48: 4000000 INFO @ Wed, 08 Dec 2021 20:26:52: 5000000 INFO @ Wed, 08 Dec 2021 20:26:56: 6000000 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 20:27:01: 7000000 INFO @ Wed, 08 Dec 2021 20:27:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976708/SRX8976708.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976708/SRX8976708.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976708/SRX8976708.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976708/SRX8976708.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 20:27:02: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:27:02: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:27:05: 8000000 INFO @ Wed, 08 Dec 2021 20:27:07: 1000000 INFO @ Wed, 08 Dec 2021 20:27:09: 9000000 INFO @ Wed, 08 Dec 2021 20:27:12: 2000000 INFO @ Wed, 08 Dec 2021 20:27:13: 10000000 INFO @ Wed, 08 Dec 2021 20:27:16: 3000000 INFO @ Wed, 08 Dec 2021 20:27:18: 11000000 INFO @ Wed, 08 Dec 2021 20:27:21: 4000000 INFO @ Wed, 08 Dec 2021 20:27:22: 12000000 INFO @ Wed, 08 Dec 2021 20:27:26: 5000000 INFO @ Wed, 08 Dec 2021 20:27:26: 13000000 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 20:27:31: 14000000 INFO @ Wed, 08 Dec 2021 20:27:31: 6000000 INFO @ Wed, 08 Dec 2021 20:27:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976708/SRX8976708.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976708/SRX8976708.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976708/SRX8976708.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976708/SRX8976708.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 20:27:32: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:27:32: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:27:35: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:27:35: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:27:35: #1 total tags in treatment: 6057682 INFO @ Wed, 08 Dec 2021 20:27:35: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:27:35: #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 20:27:35: #1 tags after filtering in treatment: 5407984 INFO @ Wed, 08 Dec 2021 20:27:35: #1 Redundant rate of treatment: 0.11 INFO @ Wed, 08 Dec 2021 20:27:35: #1 finished! INFO @ Wed, 08 Dec 2021 20:27:35: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:27:35: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:27:36: #2 number of paired peaks: 846 WARNING @ Wed, 08 Dec 2021 20:27:36: Fewer paired peaks (846) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 846 pairs to build model! INFO @ Wed, 08 Dec 2021 20:27:36: start model_add_line... INFO @ Wed, 08 Dec 2021 20:27:36: start X-correlation... INFO @ Wed, 08 Dec 2021 20:27:36: end of X-cor INFO @ Wed, 08 Dec 2021 20:27:36: #2 finished! INFO @ Wed, 08 Dec 2021 20:27:36: #2 predicted fragment length is 175 bps INFO @ Wed, 08 Dec 2021 20:27:36: #2 alternative fragment length(s) may be 4,175 bps INFO @ Wed, 08 Dec 2021 20:27:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976708/SRX8976708.05_model.r INFO @ Wed, 08 Dec 2021 20:27:36: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:27:36: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:27:36: 1000000 INFO @ Wed, 08 Dec 2021 20:27:36: 7000000 INFO @ Wed, 08 Dec 2021 20:27:40: 2000000 INFO @ Wed, 08 Dec 2021 20:27:41: 8000000 INFO @ Wed, 08 Dec 2021 20:27:45: 3000000 INFO @ Wed, 08 Dec 2021 20:27:46: 9000000 INFO @ Wed, 08 Dec 2021 20:27:48: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:27:49: 4000000 INFO @ Wed, 08 Dec 2021 20:27:51: 10000000 INFO @ Wed, 08 Dec 2021 20:27:53: 5000000 INFO @ Wed, 08 Dec 2021 20:27:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976708/SRX8976708.05_peaks.xls INFO @ Wed, 08 Dec 2021 20:27:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976708/SRX8976708.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:27:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976708/SRX8976708.05_summits.bed INFO @ Wed, 08 Dec 2021 20:27:54: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (701 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:27:56: 11000000 INFO @ Wed, 08 Dec 2021 20:27:58: 6000000 INFO @ Wed, 08 Dec 2021 20:28:01: 12000000 INFO @ Wed, 08 Dec 2021 20:28:02: 7000000 INFO @ Wed, 08 Dec 2021 20:28:06: 13000000 INFO @ Wed, 08 Dec 2021 20:28:06: 8000000 INFO @ Wed, 08 Dec 2021 20:28:11: 9000000 INFO @ Wed, 08 Dec 2021 20:28:11: 14000000 INFO @ Wed, 08 Dec 2021 20:28:15: 10000000 INFO @ Wed, 08 Dec 2021 20:28:16: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:28:16: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:28:16: #1 total tags in treatment: 6057682 INFO @ Wed, 08 Dec 2021 20:28:16: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:28:16: #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 20:28:16: #1 tags after filtering in treatment: 5407984 INFO @ Wed, 08 Dec 2021 20:28:16: #1 Redundant rate of treatment: 0.11 INFO @ Wed, 08 Dec 2021 20:28:16: #1 finished! INFO @ Wed, 08 Dec 2021 20:28:16: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:28:16: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:28:16: #2 number of paired peaks: 846 WARNING @ Wed, 08 Dec 2021 20:28:16: Fewer paired peaks (846) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 846 pairs to build model! INFO @ Wed, 08 Dec 2021 20:28:16: start model_add_line... INFO @ Wed, 08 Dec 2021 20:28:16: start X-correlation... INFO @ Wed, 08 Dec 2021 20:28:17: end of X-cor INFO @ Wed, 08 Dec 2021 20:28:17: #2 finished! INFO @ Wed, 08 Dec 2021 20:28:17: #2 predicted fragment length is 175 bps INFO @ Wed, 08 Dec 2021 20:28:17: #2 alternative fragment length(s) may be 4,175 bps INFO @ Wed, 08 Dec 2021 20:28:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976708/SRX8976708.10_model.r INFO @ Wed, 08 Dec 2021 20:28:17: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:28:17: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:28:19: 11000000 INFO @ Wed, 08 Dec 2021 20:28:24: 12000000 INFO @ Wed, 08 Dec 2021 20:28:28: 13000000 INFO @ Wed, 08 Dec 2021 20:28:29: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 20:28:32: 14000000 INFO @ Wed, 08 Dec 2021 20:28:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976708/SRX8976708.10_peaks.xls INFO @ Wed, 08 Dec 2021 20:28:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976708/SRX8976708.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:28:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976708/SRX8976708.10_summits.bed INFO @ Wed, 08 Dec 2021 20:28:35: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (415 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:28:36: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:28:36: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:28:36: #1 total tags in treatment: 6057682 INFO @ Wed, 08 Dec 2021 20:28:36: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:28:36: #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 20:28:37: #1 tags after filtering in treatment: 5407984 INFO @ Wed, 08 Dec 2021 20:28:37: #1 Redundant rate of treatment: 0.11 INFO @ Wed, 08 Dec 2021 20:28:37: #1 finished! INFO @ Wed, 08 Dec 2021 20:28:37: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:28:37: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:28:37: #2 number of paired peaks: 846 WARNING @ Wed, 08 Dec 2021 20:28:37: Fewer paired peaks (846) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 846 pairs to build model! INFO @ Wed, 08 Dec 2021 20:28:37: start model_add_line... INFO @ Wed, 08 Dec 2021 20:28:37: start X-correlation... INFO @ Wed, 08 Dec 2021 20:28:37: end of X-cor INFO @ Wed, 08 Dec 2021 20:28:37: #2 finished! INFO @ Wed, 08 Dec 2021 20:28:37: #2 predicted fragment length is 175 bps INFO @ Wed, 08 Dec 2021 20:28:37: #2 alternative fragment length(s) may be 4,175 bps INFO @ Wed, 08 Dec 2021 20:28:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976708/SRX8976708.20_model.r INFO @ Wed, 08 Dec 2021 20:28:37: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:28:37: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:28:50: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:28:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976708/SRX8976708.20_peaks.xls INFO @ Wed, 08 Dec 2021 20:28:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976708/SRX8976708.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:28:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976708/SRX8976708.20_summits.bed INFO @ Wed, 08 Dec 2021 20:28:56: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (261 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。