Job ID = 14160455 SRX = SRX9555456 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:15 8289457 reads; of these: 8289457 (100.00%) were paired; of these: 742756 (8.96%) aligned concordantly 0 times 6538982 (78.88%) aligned concordantly exactly 1 time 1007719 (12.16%) aligned concordantly >1 times ---- 742756 pairs aligned concordantly 0 times; of these: 322193 (43.38%) aligned discordantly 1 time ---- 420563 pairs aligned 0 times concordantly or discordantly; of these: 841126 mates make up the pairs; of these: 539784 (64.17%) aligned 0 times 201935 (24.01%) aligned exactly 1 time 99407 (11.82%) aligned >1 times 96.74% overall alignment rate Time searching: 00:06:16 Overall time: 00:06:16 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] 485901 / 7861592 = 0.0618 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 @ Thu, 09 Dec 2021 02:44:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9555456/SRX9555456.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9555456/SRX9555456.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9555456/SRX9555456.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9555456/SRX9555456.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 @ Thu, 09 Dec 2021 02:44:45: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:44:45: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:44:50: 1000000 INFO @ Thu, 09 Dec 2021 02:44:56: 2000000 INFO @ Thu, 09 Dec 2021 02:45:01: 3000000 INFO @ Thu, 09 Dec 2021 02:45:06: 4000000 INFO @ Thu, 09 Dec 2021 02:45:12: 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 @ Thu, 09 Dec 2021 02:45:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9555456/SRX9555456.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9555456/SRX9555456.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9555456/SRX9555456.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9555456/SRX9555456.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 @ Thu, 09 Dec 2021 02:45:15: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:45:15: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:45:17: 6000000 INFO @ Thu, 09 Dec 2021 02:45:20: 1000000 INFO @ Thu, 09 Dec 2021 02:45:22: 7000000 INFO @ Thu, 09 Dec 2021 02:45:25: 2000000 INFO @ Thu, 09 Dec 2021 02:45:28: 8000000 INFO @ Thu, 09 Dec 2021 02:45:30: 3000000 INFO @ Thu, 09 Dec 2021 02:45:33: 9000000 INFO @ Thu, 09 Dec 2021 02:45:35: 4000000 INFO @ Thu, 09 Dec 2021 02:45:39: 10000000 INFO @ Thu, 09 Dec 2021 02:45:40: 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 @ Thu, 09 Dec 2021 02:45:44: 11000000 INFO @ Thu, 09 Dec 2021 02:45:45: 6000000 INFO @ Thu, 09 Dec 2021 02:45:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9555456/SRX9555456.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9555456/SRX9555456.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9555456/SRX9555456.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9555456/SRX9555456.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 @ Thu, 09 Dec 2021 02:45:45: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:45:45: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:45:50: 7000000 INFO @ Thu, 09 Dec 2021 02:45:50: 12000000 INFO @ Thu, 09 Dec 2021 02:45:50: 1000000 INFO @ Thu, 09 Dec 2021 02:45:55: 8000000 INFO @ Thu, 09 Dec 2021 02:45:55: 2000000 INFO @ Thu, 09 Dec 2021 02:45:55: 13000000 INFO @ Thu, 09 Dec 2021 02:46:00: 9000000 INFO @ Thu, 09 Dec 2021 02:46:00: 3000000 INFO @ Thu, 09 Dec 2021 02:46:01: 14000000 INFO @ Thu, 09 Dec 2021 02:46:05: 10000000 INFO @ Thu, 09 Dec 2021 02:46:05: 4000000 INFO @ Thu, 09 Dec 2021 02:46:06: 15000000 INFO @ Thu, 09 Dec 2021 02:46:06: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 02:46:06: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 02:46:06: #1 total tags in treatment: 7072247 INFO @ Thu, 09 Dec 2021 02:46:06: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:46:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 02:46:07: #1 tags after filtering in treatment: 6684709 INFO @ Thu, 09 Dec 2021 02:46:07: #1 Redundant rate of treatment: 0.05 INFO @ Thu, 09 Dec 2021 02:46:07: #1 finished! INFO @ Thu, 09 Dec 2021 02:46:07: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:46:07: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:46:07: #2 number of paired peaks: 431 WARNING @ Thu, 09 Dec 2021 02:46:07: Fewer paired peaks (431) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 431 pairs to build model! INFO @ Thu, 09 Dec 2021 02:46:07: start model_add_line... INFO @ Thu, 09 Dec 2021 02:46:07: start X-correlation... INFO @ Thu, 09 Dec 2021 02:46:07: end of X-cor INFO @ Thu, 09 Dec 2021 02:46:07: #2 finished! INFO @ Thu, 09 Dec 2021 02:46:07: #2 predicted fragment length is 157 bps INFO @ Thu, 09 Dec 2021 02:46:07: #2 alternative fragment length(s) may be 4,157 bps INFO @ Thu, 09 Dec 2021 02:46:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9555456/SRX9555456.05_model.r INFO @ Thu, 09 Dec 2021 02:46:07: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:46:07: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:46:09: 11000000 INFO @ Thu, 09 Dec 2021 02:46:10: 5000000 INFO @ Thu, 09 Dec 2021 02:46:14: 12000000 INFO @ Thu, 09 Dec 2021 02:46:14: 6000000 INFO @ Thu, 09 Dec 2021 02:46:19: 13000000 INFO @ Thu, 09 Dec 2021 02:46:19: 7000000 INFO @ Thu, 09 Dec 2021 02:46:21: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:46:24: 14000000 INFO @ Thu, 09 Dec 2021 02:46:24: 8000000 INFO @ Thu, 09 Dec 2021 02:46:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9555456/SRX9555456.05_peaks.xls INFO @ Thu, 09 Dec 2021 02:46:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9555456/SRX9555456.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:46:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9555456/SRX9555456.05_summits.bed INFO @ Thu, 09 Dec 2021 02:46:28: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (319 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 02:46:29: 15000000 INFO @ Thu, 09 Dec 2021 02:46:29: 9000000 INFO @ Thu, 09 Dec 2021 02:46:29: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 02:46:29: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 02:46:29: #1 total tags in treatment: 7072247 INFO @ Thu, 09 Dec 2021 02:46:29: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:46:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 02:46:30: #1 tags after filtering in treatment: 6684709 INFO @ Thu, 09 Dec 2021 02:46:30: #1 Redundant rate of treatment: 0.05 INFO @ Thu, 09 Dec 2021 02:46:30: #1 finished! INFO @ Thu, 09 Dec 2021 02:46:30: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:46:30: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:46:30: #2 number of paired peaks: 431 WARNING @ Thu, 09 Dec 2021 02:46:30: Fewer paired peaks (431) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 431 pairs to build model! INFO @ Thu, 09 Dec 2021 02:46:30: start model_add_line... INFO @ Thu, 09 Dec 2021 02:46:30: start X-correlation... INFO @ Thu, 09 Dec 2021 02:46:30: end of X-cor INFO @ Thu, 09 Dec 2021 02:46:30: #2 finished! INFO @ Thu, 09 Dec 2021 02:46:30: #2 predicted fragment length is 157 bps INFO @ Thu, 09 Dec 2021 02:46:30: #2 alternative fragment length(s) may be 4,157 bps INFO @ Thu, 09 Dec 2021 02:46:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9555456/SRX9555456.10_model.r INFO @ Thu, 09 Dec 2021 02:46:30: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:46:30: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:46:34: 10000000 INFO @ Thu, 09 Dec 2021 02:46:39: 11000000 INFO @ Thu, 09 Dec 2021 02:46:43: 12000000 INFO @ Thu, 09 Dec 2021 02:46:44: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 02:46:48: 13000000 INFO @ Thu, 09 Dec 2021 02:46:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9555456/SRX9555456.10_peaks.xls INFO @ Thu, 09 Dec 2021 02:46:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9555456/SRX9555456.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:46:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9555456/SRX9555456.10_summits.bed INFO @ Thu, 09 Dec 2021 02:46:50: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (230 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 02:46:53: 14000000 INFO @ Thu, 09 Dec 2021 02:46:57: 15000000 INFO @ Thu, 09 Dec 2021 02:46:58: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 02:46:58: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 02:46:58: #1 total tags in treatment: 7072247 INFO @ Thu, 09 Dec 2021 02:46:58: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:46:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 02:46:58: #1 tags after filtering in treatment: 6684709 INFO @ Thu, 09 Dec 2021 02:46:58: #1 Redundant rate of treatment: 0.05 INFO @ Thu, 09 Dec 2021 02:46:58: #1 finished! INFO @ Thu, 09 Dec 2021 02:46:58: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:46:58: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:46:58: #2 number of paired peaks: 431 WARNING @ Thu, 09 Dec 2021 02:46:58: Fewer paired peaks (431) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 431 pairs to build model! INFO @ Thu, 09 Dec 2021 02:46:58: start model_add_line... INFO @ Thu, 09 Dec 2021 02:46:58: start X-correlation... INFO @ Thu, 09 Dec 2021 02:46:58: end of X-cor INFO @ Thu, 09 Dec 2021 02:46:58: #2 finished! INFO @ Thu, 09 Dec 2021 02:46:58: #2 predicted fragment length is 157 bps INFO @ Thu, 09 Dec 2021 02:46:58: #2 alternative fragment length(s) may be 4,157 bps INFO @ Thu, 09 Dec 2021 02:46:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9555456/SRX9555456.20_model.r INFO @ Thu, 09 Dec 2021 02:46:58: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:46:58: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:47:12: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 02:47:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9555456/SRX9555456.20_peaks.xls INFO @ Thu, 09 Dec 2021 02:47:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9555456/SRX9555456.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:47:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9555456/SRX9555456.20_summits.bed INFO @ Thu, 09 Dec 2021 02:47:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (161 records, 4 fields): 30 millis CompletedMACS2peakCalling