Job ID = 8070501 SRX = SRX8392414 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: 00:13:59 7316908 reads; of these: 7316908 (100.00%) were paired; of these: 1478434 (20.21%) aligned concordantly 0 times 4999633 (68.33%) aligned concordantly exactly 1 time 838841 (11.46%) aligned concordantly >1 times ---- 1478434 pairs aligned concordantly 0 times; of these: 419906 (28.40%) aligned discordantly 1 time ---- 1058528 pairs aligned 0 times concordantly or discordantly; of these: 2117056 mates make up the pairs; of these: 1887185 (89.14%) aligned 0 times 128546 (6.07%) aligned exactly 1 time 101325 (4.79%) aligned >1 times 87.10% overall alignment rate Time searching: 00:13:59 Overall time: 00:13:59 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] 864147 / 6219507 = 0.1389 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 08 Aug 2020 13:26:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8392414/SRX8392414.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8392414/SRX8392414.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8392414/SRX8392414.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8392414/SRX8392414.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 @ Sat, 08 Aug 2020 13:26:06: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:26:06: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:26:16: 1000000 INFO @ Sat, 08 Aug 2020 13:26:26: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 08 Aug 2020 13:26:35: 3000000 INFO @ Sat, 08 Aug 2020 13:26:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8392414/SRX8392414.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8392414/SRX8392414.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8392414/SRX8392414.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8392414/SRX8392414.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 @ Sat, 08 Aug 2020 13:26:36: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:26:36: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:26:46: 1000000 INFO @ Sat, 08 Aug 2020 13:26:46: 4000000 INFO @ Sat, 08 Aug 2020 13:26:55: 2000000 INFO @ Sat, 08 Aug 2020 13:26:57: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 08 Aug 2020 13:27:05: 3000000 INFO @ Sat, 08 Aug 2020 13:27:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8392414/SRX8392414.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8392414/SRX8392414.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8392414/SRX8392414.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8392414/SRX8392414.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 @ Sat, 08 Aug 2020 13:27:06: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:27:06: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:27:08: 6000000 INFO @ Sat, 08 Aug 2020 13:27:14: 4000000 INFO @ Sat, 08 Aug 2020 13:27:17: 1000000 INFO @ Sat, 08 Aug 2020 13:27:19: 7000000 INFO @ Sat, 08 Aug 2020 13:27:24: 5000000 INFO @ Sat, 08 Aug 2020 13:27:28: 2000000 INFO @ Sat, 08 Aug 2020 13:27:30: 8000000 INFO @ Sat, 08 Aug 2020 13:27:33: 6000000 INFO @ Sat, 08 Aug 2020 13:27:39: 3000000 INFO @ Sat, 08 Aug 2020 13:27:42: 9000000 INFO @ Sat, 08 Aug 2020 13:27:43: 7000000 INFO @ Sat, 08 Aug 2020 13:27:49: 4000000 INFO @ Sat, 08 Aug 2020 13:27:53: 8000000 INFO @ Sat, 08 Aug 2020 13:27:53: 10000000 INFO @ Sat, 08 Aug 2020 13:27:59: 5000000 INFO @ Sat, 08 Aug 2020 13:28:02: 9000000 INFO @ Sat, 08 Aug 2020 13:28:04: 11000000 INFO @ Sat, 08 Aug 2020 13:28:05: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:28:05: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:28:05: #1 total tags in treatment: 5017230 INFO @ Sat, 08 Aug 2020 13:28:05: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:28:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 13:28:05: #1 tags after filtering in treatment: 4694829 INFO @ Sat, 08 Aug 2020 13:28:05: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 08 Aug 2020 13:28:05: #1 finished! INFO @ Sat, 08 Aug 2020 13:28:05: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:28:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:28:05: #2 number of paired peaks: 459 WARNING @ Sat, 08 Aug 2020 13:28:05: Fewer paired peaks (459) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 459 pairs to build model! INFO @ Sat, 08 Aug 2020 13:28:05: start model_add_line... INFO @ Sat, 08 Aug 2020 13:28:05: start X-correlation... INFO @ Sat, 08 Aug 2020 13:28:05: end of X-cor INFO @ Sat, 08 Aug 2020 13:28:05: #2 finished! INFO @ Sat, 08 Aug 2020 13:28:05: #2 predicted fragment length is 213 bps INFO @ Sat, 08 Aug 2020 13:28:05: #2 alternative fragment length(s) may be 213 bps INFO @ Sat, 08 Aug 2020 13:28:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8392414/SRX8392414.05_model.r WARNING @ Sat, 08 Aug 2020 13:28:05: #2 Since the d (213) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:28:05: #2 You may need to consider one of the other alternative d(s): 213 WARNING @ Sat, 08 Aug 2020 13:28:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 13:28:05: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:28:05: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 13:28:09: 6000000 INFO @ Sat, 08 Aug 2020 13:28:12: 10000000 INFO @ Sat, 08 Aug 2020 13:28:16: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:28:18: 7000000 INFO @ Sat, 08 Aug 2020 13:28:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8392414/SRX8392414.05_peaks.xls INFO @ Sat, 08 Aug 2020 13:28:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8392414/SRX8392414.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:28:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8392414/SRX8392414.05_summits.bed INFO @ Sat, 08 Aug 2020 13:28:21: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (337 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:28:21: 11000000 INFO @ Sat, 08 Aug 2020 13:28:21: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:28:21: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:28:21: #1 total tags in treatment: 5017230 INFO @ Sat, 08 Aug 2020 13:28:21: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:28:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 13:28:21: #1 tags after filtering in treatment: 4694829 INFO @ Sat, 08 Aug 2020 13:28:21: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 08 Aug 2020 13:28:21: #1 finished! INFO @ Sat, 08 Aug 2020 13:28:21: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:28:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:28:22: #2 number of paired peaks: 459 WARNING @ Sat, 08 Aug 2020 13:28:22: Fewer paired peaks (459) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 459 pairs to build model! INFO @ Sat, 08 Aug 2020 13:28:22: start model_add_line... INFO @ Sat, 08 Aug 2020 13:28:22: start X-correlation... INFO @ Sat, 08 Aug 2020 13:28:22: end of X-cor INFO @ Sat, 08 Aug 2020 13:28:22: #2 finished! INFO @ Sat, 08 Aug 2020 13:28:22: #2 predicted fragment length is 213 bps INFO @ Sat, 08 Aug 2020 13:28:22: #2 alternative fragment length(s) may be 213 bps INFO @ Sat, 08 Aug 2020 13:28:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8392414/SRX8392414.10_model.r WARNING @ Sat, 08 Aug 2020 13:28:22: #2 Since the d (213) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:28:22: #2 You may need to consider one of the other alternative d(s): 213 WARNING @ Sat, 08 Aug 2020 13:28:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 13:28:22: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:28:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:28:27: 8000000 BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 13:28:33: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:28:35: 9000000 INFO @ Sat, 08 Aug 2020 13:28:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8392414/SRX8392414.10_peaks.xls INFO @ Sat, 08 Aug 2020 13:28:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8392414/SRX8392414.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:28:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8392414/SRX8392414.10_summits.bed INFO @ Sat, 08 Aug 2020 13:28:37: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (244 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:28:43: 10000000 INFO @ Sat, 08 Aug 2020 13:28:50: 11000000 INFO @ Sat, 08 Aug 2020 13:28:50: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:28:50: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:28:50: #1 total tags in treatment: 5017230 INFO @ Sat, 08 Aug 2020 13:28:50: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:28:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 13:28:50: #1 tags after filtering in treatment: 4694829 INFO @ Sat, 08 Aug 2020 13:28:50: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 08 Aug 2020 13:28:50: #1 finished! INFO @ Sat, 08 Aug 2020 13:28:50: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:28:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:28:51: #2 number of paired peaks: 459 WARNING @ Sat, 08 Aug 2020 13:28:51: Fewer paired peaks (459) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 459 pairs to build model! INFO @ Sat, 08 Aug 2020 13:28:51: start model_add_line... INFO @ Sat, 08 Aug 2020 13:28:51: start X-correlation... INFO @ Sat, 08 Aug 2020 13:28:51: end of X-cor INFO @ Sat, 08 Aug 2020 13:28:51: #2 finished! INFO @ Sat, 08 Aug 2020 13:28:51: #2 predicted fragment length is 213 bps INFO @ Sat, 08 Aug 2020 13:28:51: #2 alternative fragment length(s) may be 213 bps INFO @ Sat, 08 Aug 2020 13:28:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8392414/SRX8392414.20_model.r WARNING @ Sat, 08 Aug 2020 13:28:51: #2 Since the d (213) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:28:51: #2 You may need to consider one of the other alternative d(s): 213 WARNING @ Sat, 08 Aug 2020 13:28:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 13:28:51: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:28:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:29:02: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:29:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8392414/SRX8392414.20_peaks.xls INFO @ Sat, 08 Aug 2020 13:29:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8392414/SRX8392414.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:29:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8392414/SRX8392414.20_summits.bed INFO @ Sat, 08 Aug 2020 13:29:07: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (178 records, 4 fields): 1 millis CompletedMACS2peakCalling