Job ID = 10165902 SRX = SRX6799192 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: 00:10:08 34221432 reads; of these: 34221432 (100.00%) were unpaired; of these: 1677554 (4.90%) aligned 0 times 22403764 (65.47%) aligned exactly 1 time 10140114 (29.63%) aligned >1 times 95.10% overall alignment rate Time searching: 00:10:08 Overall time: 00:10:08 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 16 files... [bam_rmdupse_core] 10713952 / 32543878 = 0.3292 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 @ Thu, 08 Oct 2020 20:24:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6799192/SRX6799192.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6799192/SRX6799192.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6799192/SRX6799192.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6799192/SRX6799192.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, 08 Oct 2020 20:24:08: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:24:08: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:24:14: 1000000 INFO @ Thu, 08 Oct 2020 20:24:19: 2000000 INFO @ Thu, 08 Oct 2020 20:24:24: 3000000 INFO @ Thu, 08 Oct 2020 20:24:30: 4000000 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 @ Thu, 08 Oct 2020 20:24:35: 5000000 INFO @ Thu, 08 Oct 2020 20:24:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6799192/SRX6799192.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6799192/SRX6799192.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6799192/SRX6799192.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6799192/SRX6799192.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, 08 Oct 2020 20:24:38: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:24:38: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:24:41: 6000000 INFO @ Thu, 08 Oct 2020 20:24:45: 1000000 INFO @ Thu, 08 Oct 2020 20:24:47: 7000000 INFO @ Thu, 08 Oct 2020 20:24:50: 2000000 INFO @ Thu, 08 Oct 2020 20:24:53: 8000000 INFO @ Thu, 08 Oct 2020 20:24:56: 3000000 INFO @ Thu, 08 Oct 2020 20:24:59: 9000000 INFO @ Thu, 08 Oct 2020 20:25:02: 4000000 INFO @ Thu, 08 Oct 2020 20:25:04: 10000000 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 @ Thu, 08 Oct 2020 20:25:09: 5000000 INFO @ Thu, 08 Oct 2020 20:25:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6799192/SRX6799192.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6799192/SRX6799192.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6799192/SRX6799192.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6799192/SRX6799192.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, 08 Oct 2020 20:25:09: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:25:09: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:25:10: 11000000 INFO @ Thu, 08 Oct 2020 20:25:15: 6000000 INFO @ Thu, 08 Oct 2020 20:25:15: 1000000 INFO @ Thu, 08 Oct 2020 20:25:16: 12000000 INFO @ Thu, 08 Oct 2020 20:25:21: 2000000 INFO @ Thu, 08 Oct 2020 20:25:21: 7000000 INFO @ Thu, 08 Oct 2020 20:25:22: 13000000 INFO @ Thu, 08 Oct 2020 20:25:27: 3000000 INFO @ Thu, 08 Oct 2020 20:25:27: 8000000 INFO @ Thu, 08 Oct 2020 20:25:28: 14000000 INFO @ Thu, 08 Oct 2020 20:25:33: 4000000 INFO @ Thu, 08 Oct 2020 20:25:33: 9000000 INFO @ Thu, 08 Oct 2020 20:25:34: 15000000 INFO @ Thu, 08 Oct 2020 20:25:39: 5000000 INFO @ Thu, 08 Oct 2020 20:25:39: 10000000 INFO @ Thu, 08 Oct 2020 20:25:40: 16000000 INFO @ Thu, 08 Oct 2020 20:25:45: 6000000 INFO @ Thu, 08 Oct 2020 20:25:45: 11000000 INFO @ Thu, 08 Oct 2020 20:25:46: 17000000 INFO @ Thu, 08 Oct 2020 20:25:51: 7000000 INFO @ Thu, 08 Oct 2020 20:25:51: 12000000 INFO @ Thu, 08 Oct 2020 20:25:52: 18000000 INFO @ Thu, 08 Oct 2020 20:25:57: 8000000 INFO @ Thu, 08 Oct 2020 20:25:57: 13000000 INFO @ Thu, 08 Oct 2020 20:25:58: 19000000 INFO @ Thu, 08 Oct 2020 20:26:03: 9000000 INFO @ Thu, 08 Oct 2020 20:26:04: 14000000 INFO @ Thu, 08 Oct 2020 20:26:04: 20000000 INFO @ Thu, 08 Oct 2020 20:26:09: 10000000 INFO @ Thu, 08 Oct 2020 20:26:10: 15000000 INFO @ Thu, 08 Oct 2020 20:26:10: 21000000 INFO @ Thu, 08 Oct 2020 20:26:15: 11000000 INFO @ Thu, 08 Oct 2020 20:26:15: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:26:15: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:26:15: #1 total tags in treatment: 21829926 INFO @ Thu, 08 Oct 2020 20:26:15: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:26:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:26:16: #1 tags after filtering in treatment: 21829926 INFO @ Thu, 08 Oct 2020 20:26:16: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:26:16: #1 finished! INFO @ Thu, 08 Oct 2020 20:26:16: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:26:16: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:26:16: 16000000 INFO @ Thu, 08 Oct 2020 20:26:17: #2 number of paired peaks: 424 WARNING @ Thu, 08 Oct 2020 20:26:17: Fewer paired peaks (424) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 424 pairs to build model! INFO @ Thu, 08 Oct 2020 20:26:17: start model_add_line... INFO @ Thu, 08 Oct 2020 20:26:17: start X-correlation... INFO @ Thu, 08 Oct 2020 20:26:17: end of X-cor INFO @ Thu, 08 Oct 2020 20:26:17: #2 finished! INFO @ Thu, 08 Oct 2020 20:26:17: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:26:17: #2 alternative fragment length(s) may be 1,17,42 bps INFO @ Thu, 08 Oct 2020 20:26:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6799192/SRX6799192.05_model.r WARNING @ Thu, 08 Oct 2020 20:26:17: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:26:17: #2 You may need to consider one of the other alternative d(s): 1,17,42 WARNING @ Thu, 08 Oct 2020 20:26:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:26:17: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:26:17: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:26:21: 12000000 INFO @ Thu, 08 Oct 2020 20:26:22: 17000000 INFO @ Thu, 08 Oct 2020 20:26:27: 13000000 INFO @ Thu, 08 Oct 2020 20:26:28: 18000000 INFO @ Thu, 08 Oct 2020 20:26:33: 14000000 INFO @ Thu, 08 Oct 2020 20:26:34: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:26:39: 15000000 INFO @ Thu, 08 Oct 2020 20:26:40: 20000000 INFO @ Thu, 08 Oct 2020 20:26:45: 16000000 INFO @ Thu, 08 Oct 2020 20:26:46: 21000000 INFO @ Thu, 08 Oct 2020 20:26:49: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:26:51: 17000000 INFO @ Thu, 08 Oct 2020 20:26:51: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:26:51: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:26:51: #1 total tags in treatment: 21829926 INFO @ Thu, 08 Oct 2020 20:26:51: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:26:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:26:52: #1 tags after filtering in treatment: 21829926 INFO @ Thu, 08 Oct 2020 20:26:52: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:26:52: #1 finished! INFO @ Thu, 08 Oct 2020 20:26:52: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:26:52: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:26:53: #2 number of paired peaks: 424 WARNING @ Thu, 08 Oct 2020 20:26:53: Fewer paired peaks (424) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 424 pairs to build model! INFO @ Thu, 08 Oct 2020 20:26:53: start model_add_line... INFO @ Thu, 08 Oct 2020 20:26:53: start X-correlation... INFO @ Thu, 08 Oct 2020 20:26:53: end of X-cor INFO @ Thu, 08 Oct 2020 20:26:53: #2 finished! INFO @ Thu, 08 Oct 2020 20:26:53: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:26:53: #2 alternative fragment length(s) may be 1,17,42 bps INFO @ Thu, 08 Oct 2020 20:26:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6799192/SRX6799192.10_model.r WARNING @ Thu, 08 Oct 2020 20:26:53: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:26:53: #2 You may need to consider one of the other alternative d(s): 1,17,42 WARNING @ Thu, 08 Oct 2020 20:26:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:26:53: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:26:53: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:26:56: 18000000 INFO @ Thu, 08 Oct 2020 20:27:02: 19000000 INFO @ Thu, 08 Oct 2020 20:27:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6799192/SRX6799192.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:27:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6799192/SRX6799192.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:27:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6799192/SRX6799192.05_summits.bed INFO @ Thu, 08 Oct 2020 20:27:04: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:27:07: 20000000 INFO @ Thu, 08 Oct 2020 20:27:13: 21000000 INFO @ Thu, 08 Oct 2020 20:27:17: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:27:17: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:27:17: #1 total tags in treatment: 21829926 INFO @ Thu, 08 Oct 2020 20:27:17: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:27:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:27:18: #1 tags after filtering in treatment: 21829926 INFO @ Thu, 08 Oct 2020 20:27:18: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:27:18: #1 finished! INFO @ Thu, 08 Oct 2020 20:27:18: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:27:18: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:27:19: #2 number of paired peaks: 424 WARNING @ Thu, 08 Oct 2020 20:27:19: Fewer paired peaks (424) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 424 pairs to build model! INFO @ Thu, 08 Oct 2020 20:27:19: start model_add_line... INFO @ Thu, 08 Oct 2020 20:27:19: start X-correlation... INFO @ Thu, 08 Oct 2020 20:27:19: end of X-cor INFO @ Thu, 08 Oct 2020 20:27:19: #2 finished! INFO @ Thu, 08 Oct 2020 20:27:19: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:27:19: #2 alternative fragment length(s) may be 1,17,42 bps INFO @ Thu, 08 Oct 2020 20:27:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6799192/SRX6799192.20_model.r WARNING @ Thu, 08 Oct 2020 20:27:19: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:27:19: #2 You may need to consider one of the other alternative d(s): 1,17,42 WARNING @ Thu, 08 Oct 2020 20:27:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:27:19: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:27:19: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:27:24: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:27:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6799192/SRX6799192.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:27:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6799192/SRX6799192.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:27:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6799192/SRX6799192.10_summits.bed INFO @ Thu, 08 Oct 2020 20:27:39: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:27:51: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:28:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6799192/SRX6799192.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:28:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6799192/SRX6799192.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:28:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6799192/SRX6799192.20_summits.bed INFO @ Thu, 08 Oct 2020 20:28:06: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling