Job ID = 16433642 SRX = SRX15407781 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: 00:05:49 19171822 reads; of these: 19171822 (100.00%) were unpaired; of these: 1586831 (8.28%) aligned 0 times 15250932 (79.55%) aligned exactly 1 time 2334059 (12.17%) aligned >1 times 91.72% overall alignment rate Time searching: 00:05:49 Overall time: 00:05:49 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] 2853364 / 17584991 = 0.1623 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 09:54:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX15407781/SRX15407781.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX15407781/SRX15407781.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX15407781/SRX15407781.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX15407781/SRX15407781.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 @ Tue, 02 Aug 2022 09:54:04: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:54:04: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:54:09: 1000000 INFO @ Tue, 02 Aug 2022 09:54:14: 2000000 INFO @ Tue, 02 Aug 2022 09:54:19: 3000000 INFO @ Tue, 02 Aug 2022 09:54:24: 4000000 INFO @ Tue, 02 Aug 2022 09:54:29: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 09:54:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX15407781/SRX15407781.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX15407781/SRX15407781.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX15407781/SRX15407781.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX15407781/SRX15407781.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 @ Tue, 02 Aug 2022 09:54:34: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:54:34: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:54:34: 6000000 INFO @ Tue, 02 Aug 2022 09:54:39: 7000000 INFO @ Tue, 02 Aug 2022 09:54:40: 1000000 INFO @ Tue, 02 Aug 2022 09:54:45: 8000000 INFO @ Tue, 02 Aug 2022 09:54:47: 2000000 INFO @ Tue, 02 Aug 2022 09:54:50: 9000000 INFO @ Tue, 02 Aug 2022 09:54:53: 3000000 INFO @ Tue, 02 Aug 2022 09:54:55: 10000000 INFO @ Tue, 02 Aug 2022 09:54:59: 4000000 INFO @ Tue, 02 Aug 2022 09:55:01: 11000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 09:55:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX15407781/SRX15407781.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX15407781/SRX15407781.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX15407781/SRX15407781.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX15407781/SRX15407781.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 @ Tue, 02 Aug 2022 09:55:04: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:55:04: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:55:05: 5000000 INFO @ Tue, 02 Aug 2022 09:55:06: 12000000 INFO @ Tue, 02 Aug 2022 09:55:09: 1000000 INFO @ Tue, 02 Aug 2022 09:55:11: 6000000 INFO @ Tue, 02 Aug 2022 09:55:11: 13000000 INFO @ Tue, 02 Aug 2022 09:55:16: 2000000 INFO @ Tue, 02 Aug 2022 09:55:17: 14000000 INFO @ Tue, 02 Aug 2022 09:55:17: 7000000 INFO @ Tue, 02 Aug 2022 09:55:21: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:55:21: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:55:21: #1 total tags in treatment: 14731627 INFO @ Tue, 02 Aug 2022 09:55:21: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:55:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 09:55:21: #1 tags after filtering in treatment: 14731627 INFO @ Tue, 02 Aug 2022 09:55:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:55:21: #1 finished! INFO @ Tue, 02 Aug 2022 09:55:21: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:55:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:55:22: #2 number of paired peaks: 625 WARNING @ Tue, 02 Aug 2022 09:55:22: Fewer paired peaks (625) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 625 pairs to build model! INFO @ Tue, 02 Aug 2022 09:55:22: start model_add_line... INFO @ Tue, 02 Aug 2022 09:55:22: start X-correlation... INFO @ Tue, 02 Aug 2022 09:55:22: end of X-cor INFO @ Tue, 02 Aug 2022 09:55:22: #2 finished! INFO @ Tue, 02 Aug 2022 09:55:22: #2 predicted fragment length is 166 bps INFO @ Tue, 02 Aug 2022 09:55:22: #2 alternative fragment length(s) may be 166 bps INFO @ Tue, 02 Aug 2022 09:55:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX15407781/SRX15407781.05_model.r INFO @ Tue, 02 Aug 2022 09:55:22: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:55:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:55:22: 3000000 INFO @ Tue, 02 Aug 2022 09:55:22: 8000000 INFO @ Tue, 02 Aug 2022 09:55:27: 9000000 INFO @ Tue, 02 Aug 2022 09:55:28: 4000000 INFO @ Tue, 02 Aug 2022 09:55:33: 10000000 INFO @ Tue, 02 Aug 2022 09:55:35: 5000000 INFO @ Tue, 02 Aug 2022 09:55:38: 11000000 INFO @ Tue, 02 Aug 2022 09:55:41: 6000000 INFO @ Tue, 02 Aug 2022 09:55:44: 12000000 INFO @ Tue, 02 Aug 2022 09:55:47: 7000000 INFO @ Tue, 02 Aug 2022 09:55:49: 13000000 INFO @ Tue, 02 Aug 2022 09:55:52: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:55:54: 8000000 INFO @ Tue, 02 Aug 2022 09:55:54: 14000000 INFO @ Tue, 02 Aug 2022 09:55:58: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:55:58: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:55:58: #1 total tags in treatment: 14731627 INFO @ Tue, 02 Aug 2022 09:55:58: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:55:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 09:55:58: #1 tags after filtering in treatment: 14731627 INFO @ Tue, 02 Aug 2022 09:55:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:55:58: #1 finished! INFO @ Tue, 02 Aug 2022 09:55:58: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:55:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:55:59: #2 number of paired peaks: 625 WARNING @ Tue, 02 Aug 2022 09:55:59: Fewer paired peaks (625) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 625 pairs to build model! INFO @ Tue, 02 Aug 2022 09:55:59: start model_add_line... INFO @ Tue, 02 Aug 2022 09:56:00: start X-correlation... INFO @ Tue, 02 Aug 2022 09:56:00: end of X-cor INFO @ Tue, 02 Aug 2022 09:56:00: #2 finished! INFO @ Tue, 02 Aug 2022 09:56:00: #2 predicted fragment length is 166 bps INFO @ Tue, 02 Aug 2022 09:56:00: #2 alternative fragment length(s) may be 166 bps INFO @ Tue, 02 Aug 2022 09:56:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX15407781/SRX15407781.10_model.r INFO @ Tue, 02 Aug 2022 09:56:00: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:56:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:56:00: 9000000 INFO @ Tue, 02 Aug 2022 09:56:06: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 09:56:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX15407781/SRX15407781.05_peaks.xls INFO @ Tue, 02 Aug 2022 09:56:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX15407781/SRX15407781.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:56:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX15407781/SRX15407781.05_summits.bed INFO @ Tue, 02 Aug 2022 09:56:08: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (7992 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 09:56:12: 11000000 INFO @ Tue, 02 Aug 2022 09:56:18: 12000000 INFO @ Tue, 02 Aug 2022 09:56:24: 13000000 INFO @ Tue, 02 Aug 2022 09:56:30: 14000000 INFO @ Tue, 02 Aug 2022 09:56:31: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:56:35: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:56:35: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:56:35: #1 total tags in treatment: 14731627 INFO @ Tue, 02 Aug 2022 09:56:35: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:56:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 09:56:35: #1 tags after filtering in treatment: 14731627 INFO @ Tue, 02 Aug 2022 09:56:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:56:35: #1 finished! INFO @ Tue, 02 Aug 2022 09:56:35: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:56:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:56:36: #2 number of paired peaks: 625 WARNING @ Tue, 02 Aug 2022 09:56:36: Fewer paired peaks (625) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 625 pairs to build model! INFO @ Tue, 02 Aug 2022 09:56:36: start model_add_line... INFO @ Tue, 02 Aug 2022 09:56:36: start X-correlation... INFO @ Tue, 02 Aug 2022 09:56:36: end of X-cor INFO @ Tue, 02 Aug 2022 09:56:36: #2 finished! INFO @ Tue, 02 Aug 2022 09:56:36: #2 predicted fragment length is 166 bps INFO @ Tue, 02 Aug 2022 09:56:36: #2 alternative fragment length(s) may be 166 bps INFO @ Tue, 02 Aug 2022 09:56:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX15407781/SRX15407781.20_model.r INFO @ Tue, 02 Aug 2022 09:56:36: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:56:36: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 09:56:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX15407781/SRX15407781.10_peaks.xls INFO @ Tue, 02 Aug 2022 09:56:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX15407781/SRX15407781.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:56:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX15407781/SRX15407781.10_summits.bed INFO @ Tue, 02 Aug 2022 09:56:47: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5648 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 09:57:06: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:57:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX15407781/SRX15407781.20_peaks.xls INFO @ Tue, 02 Aug 2022 09:57:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX15407781/SRX15407781.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:57:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX15407781/SRX15407781.20_summits.bed INFO @ Tue, 02 Aug 2022 09:57:21: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3389 records, 4 fields): 19 millis CompletedMACS2peakCalling