Job ID = 14158399 SRX = SRX7739518 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE 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: 00:04:17 19622836 reads; of these: 19622836 (100.00%) were unpaired; of these: 459743 (2.34%) aligned 0 times 16135112 (82.23%) aligned exactly 1 time 3027981 (15.43%) aligned >1 times 97.66% overall alignment rate Time searching: 00:04:17 Overall time: 00:04:17 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_rmdupse_core] 3072872 / 19163093 = 0.1604 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 17:31:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7739518/SRX7739518.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7739518/SRX7739518.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7739518/SRX7739518.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7739518/SRX7739518.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 17:31:04: #1 read tag files... INFO @ Wed, 08 Dec 2021 17:31:04: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 17:31:11: 1000000 INFO @ Wed, 08 Dec 2021 17:31:16: 2000000 INFO @ Wed, 08 Dec 2021 17:31:22: 3000000 INFO @ Wed, 08 Dec 2021 17:31:28: 4000000 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 17:31:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7739518/SRX7739518.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7739518/SRX7739518.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7739518/SRX7739518.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7739518/SRX7739518.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 17:31:34: #1 read tag files... INFO @ Wed, 08 Dec 2021 17:31:34: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 17:31:34: 5000000 INFO @ Wed, 08 Dec 2021 17:31:39: 1000000 INFO @ Wed, 08 Dec 2021 17:31:41: 6000000 INFO @ Wed, 08 Dec 2021 17:31:45: 2000000 INFO @ Wed, 08 Dec 2021 17:31:47: 7000000 INFO @ Wed, 08 Dec 2021 17:31:50: 3000000 INFO @ Wed, 08 Dec 2021 17:31:53: 8000000 INFO @ Wed, 08 Dec 2021 17:31:56: 4000000 INFO @ Wed, 08 Dec 2021 17:31:59: 9000000 INFO @ Wed, 08 Dec 2021 17:32:01: 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 17:32:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7739518/SRX7739518.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7739518/SRX7739518.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7739518/SRX7739518.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7739518/SRX7739518.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 17:32:04: #1 read tag files... INFO @ Wed, 08 Dec 2021 17:32:04: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 17:32:05: 10000000 INFO @ Wed, 08 Dec 2021 17:32:07: 6000000 INFO @ Wed, 08 Dec 2021 17:32:10: 1000000 INFO @ Wed, 08 Dec 2021 17:32:12: 11000000 INFO @ Wed, 08 Dec 2021 17:32:12: 7000000 INFO @ Wed, 08 Dec 2021 17:32:16: 2000000 INFO @ Wed, 08 Dec 2021 17:32:18: 8000000 INFO @ Wed, 08 Dec 2021 17:32:18: 12000000 INFO @ Wed, 08 Dec 2021 17:32:23: 3000000 INFO @ Wed, 08 Dec 2021 17:32:23: 9000000 INFO @ Wed, 08 Dec 2021 17:32:25: 13000000 INFO @ Wed, 08 Dec 2021 17:32:29: 10000000 INFO @ Wed, 08 Dec 2021 17:32:29: 4000000 INFO @ Wed, 08 Dec 2021 17:32:31: 14000000 INFO @ Wed, 08 Dec 2021 17:32:34: 11000000 INFO @ Wed, 08 Dec 2021 17:32:35: 5000000 INFO @ Wed, 08 Dec 2021 17:32:37: 15000000 INFO @ Wed, 08 Dec 2021 17:32:40: 12000000 INFO @ Wed, 08 Dec 2021 17:32:42: 6000000 INFO @ Wed, 08 Dec 2021 17:32:43: 16000000 INFO @ Wed, 08 Dec 2021 17:32:44: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 17:32:44: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 17:32:44: #1 total tags in treatment: 16090221 INFO @ Wed, 08 Dec 2021 17:32:44: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 17:32:44: #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 17:32:44: #1 tags after filtering in treatment: 16090221 INFO @ Wed, 08 Dec 2021 17:32:44: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 17:32:44: #1 finished! INFO @ Wed, 08 Dec 2021 17:32:44: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 17:32:44: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 17:32:45: 13000000 INFO @ Wed, 08 Dec 2021 17:32:45: #2 number of paired peaks: 306 WARNING @ Wed, 08 Dec 2021 17:32:45: Fewer paired peaks (306) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 306 pairs to build model! INFO @ Wed, 08 Dec 2021 17:32:45: start model_add_line... INFO @ Wed, 08 Dec 2021 17:32:45: start X-correlation... INFO @ Wed, 08 Dec 2021 17:32:46: end of X-cor INFO @ Wed, 08 Dec 2021 17:32:46: #2 finished! INFO @ Wed, 08 Dec 2021 17:32:46: #2 predicted fragment length is 103 bps INFO @ Wed, 08 Dec 2021 17:32:46: #2 alternative fragment length(s) may be 3,103 bps INFO @ Wed, 08 Dec 2021 17:32:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7739518/SRX7739518.05_model.r INFO @ Wed, 08 Dec 2021 17:32:46: #3 Call peaks... INFO @ Wed, 08 Dec 2021 17:32:46: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 17:32:48: 7000000 INFO @ Wed, 08 Dec 2021 17:32:51: 14000000 INFO @ Wed, 08 Dec 2021 17:32:54: 8000000 INFO @ Wed, 08 Dec 2021 17:32:56: 15000000 INFO @ Wed, 08 Dec 2021 17:33:00: 9000000 INFO @ Wed, 08 Dec 2021 17:33:02: 16000000 INFO @ Wed, 08 Dec 2021 17:33:02: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 17:33:02: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 17:33:02: #1 total tags in treatment: 16090221 INFO @ Wed, 08 Dec 2021 17:33:02: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 17:33:02: #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 17:33:03: #1 tags after filtering in treatment: 16090221 INFO @ Wed, 08 Dec 2021 17:33:03: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 17:33:03: #1 finished! INFO @ Wed, 08 Dec 2021 17:33:03: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 17:33:03: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 17:33:04: #2 number of paired peaks: 306 WARNING @ Wed, 08 Dec 2021 17:33:04: Fewer paired peaks (306) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 306 pairs to build model! INFO @ Wed, 08 Dec 2021 17:33:04: start model_add_line... INFO @ Wed, 08 Dec 2021 17:33:04: start X-correlation... INFO @ Wed, 08 Dec 2021 17:33:04: end of X-cor INFO @ Wed, 08 Dec 2021 17:33:04: #2 finished! INFO @ Wed, 08 Dec 2021 17:33:04: #2 predicted fragment length is 103 bps INFO @ Wed, 08 Dec 2021 17:33:04: #2 alternative fragment length(s) may be 3,103 bps INFO @ Wed, 08 Dec 2021 17:33:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7739518/SRX7739518.10_model.r INFO @ Wed, 08 Dec 2021 17:33:04: #3 Call peaks... INFO @ Wed, 08 Dec 2021 17:33:04: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 17:33:06: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 17:33:12: 11000000 INFO @ Wed, 08 Dec 2021 17:33:16: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 17:33:17: 12000000 INFO @ Wed, 08 Dec 2021 17:33:23: 13000000 INFO @ Wed, 08 Dec 2021 17:33:29: 14000000 INFO @ Wed, 08 Dec 2021 17:33:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7739518/SRX7739518.05_peaks.xls INFO @ Wed, 08 Dec 2021 17:33:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7739518/SRX7739518.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 17:33:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7739518/SRX7739518.05_summits.bed INFO @ Wed, 08 Dec 2021 17:33:31: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1954 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 17:33:33: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 17:33:35: 15000000 INFO @ Wed, 08 Dec 2021 17:33:41: 16000000 INFO @ Wed, 08 Dec 2021 17:33:41: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 17:33:41: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 17:33:41: #1 total tags in treatment: 16090221 INFO @ Wed, 08 Dec 2021 17:33:41: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 17:33:41: #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 17:33:42: #1 tags after filtering in treatment: 16090221 INFO @ Wed, 08 Dec 2021 17:33:42: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 17:33:42: #1 finished! INFO @ Wed, 08 Dec 2021 17:33:42: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 17:33:42: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 17:33:43: #2 number of paired peaks: 306 WARNING @ Wed, 08 Dec 2021 17:33:43: Fewer paired peaks (306) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 306 pairs to build model! INFO @ Wed, 08 Dec 2021 17:33:43: start model_add_line... INFO @ Wed, 08 Dec 2021 17:33:43: start X-correlation... INFO @ Wed, 08 Dec 2021 17:33:43: end of X-cor INFO @ Wed, 08 Dec 2021 17:33:43: #2 finished! INFO @ Wed, 08 Dec 2021 17:33:43: #2 predicted fragment length is 103 bps INFO @ Wed, 08 Dec 2021 17:33:43: #2 alternative fragment length(s) may be 3,103 bps INFO @ Wed, 08 Dec 2021 17:33:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7739518/SRX7739518.20_model.r INFO @ Wed, 08 Dec 2021 17:33:43: #3 Call peaks... INFO @ Wed, 08 Dec 2021 17:33:43: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 17:33:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7739518/SRX7739518.10_peaks.xls INFO @ Wed, 08 Dec 2021 17:33:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7739518/SRX7739518.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 17:33:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7739518/SRX7739518.10_summits.bed INFO @ Wed, 08 Dec 2021 17:33:48: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (933 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 17:34:11: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 17:34:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7739518/SRX7739518.20_peaks.xls INFO @ Wed, 08 Dec 2021 17:34:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7739518/SRX7739518.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 17:34:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7739518/SRX7739518.20_summits.bed INFO @ Wed, 08 Dec 2021 17:34:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (429 records, 4 fields): 1 millis CompletedMACS2peakCalling