Job ID = 6626607 SRX = SRX7630549 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: 00:06:12 37184627 reads; of these: 37184627 (100.00%) were unpaired; of these: 13336960 (35.87%) aligned 0 times 19830727 (53.33%) aligned exactly 1 time 4016940 (10.80%) aligned >1 times 64.13% overall alignment rate Time searching: 00:06:12 Overall time: 00:06:12 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_rmdupse_core] 7082306 / 23847667 = 0.2970 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 @ Tue, 14 Jul 2020 08:01:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7630549/SRX7630549.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7630549/SRX7630549.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7630549/SRX7630549.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7630549/SRX7630549.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, 14 Jul 2020 08:01:24: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:01:24: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:01:29: 1000000 INFO @ Tue, 14 Jul 2020 08:01:34: 2000000 INFO @ Tue, 14 Jul 2020 08:01:39: 3000000 INFO @ Tue, 14 Jul 2020 08:01:44: 4000000 INFO @ Tue, 14 Jul 2020 08:01:49: 5000000 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 @ Tue, 14 Jul 2020 08:01:54: 6000000 INFO @ Tue, 14 Jul 2020 08:01:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7630549/SRX7630549.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7630549/SRX7630549.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7630549/SRX7630549.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7630549/SRX7630549.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, 14 Jul 2020 08:01:54: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:01:54: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:01:59: 7000000 INFO @ Tue, 14 Jul 2020 08:01:59: 1000000 INFO @ Tue, 14 Jul 2020 08:02:04: 8000000 INFO @ Tue, 14 Jul 2020 08:02:04: 2000000 INFO @ Tue, 14 Jul 2020 08:02:09: 9000000 INFO @ Tue, 14 Jul 2020 08:02:09: 3000000 INFO @ Tue, 14 Jul 2020 08:02:14: 10000000 INFO @ Tue, 14 Jul 2020 08:02:14: 4000000 INFO @ Tue, 14 Jul 2020 08:02:19: 11000000 INFO @ Tue, 14 Jul 2020 08:02:19: 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 @ Tue, 14 Jul 2020 08:02:24: 12000000 INFO @ Tue, 14 Jul 2020 08:02:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7630549/SRX7630549.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7630549/SRX7630549.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7630549/SRX7630549.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7630549/SRX7630549.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, 14 Jul 2020 08:02:24: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:02:24: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:02:24: 6000000 INFO @ Tue, 14 Jul 2020 08:02:29: 13000000 INFO @ Tue, 14 Jul 2020 08:02:29: 1000000 INFO @ Tue, 14 Jul 2020 08:02:29: 7000000 INFO @ Tue, 14 Jul 2020 08:02:34: 14000000 INFO @ Tue, 14 Jul 2020 08:02:35: 8000000 INFO @ Tue, 14 Jul 2020 08:02:35: 2000000 INFO @ Tue, 14 Jul 2020 08:02:39: 15000000 INFO @ Tue, 14 Jul 2020 08:02:40: 9000000 INFO @ Tue, 14 Jul 2020 08:02:40: 3000000 INFO @ Tue, 14 Jul 2020 08:02:44: 16000000 INFO @ Tue, 14 Jul 2020 08:02:45: 10000000 INFO @ Tue, 14 Jul 2020 08:02:45: 4000000 INFO @ Tue, 14 Jul 2020 08:02:48: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 08:02:48: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 08:02:48: #1 total tags in treatment: 16765361 INFO @ Tue, 14 Jul 2020 08:02:48: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:02:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:02:48: #1 tags after filtering in treatment: 16765361 INFO @ Tue, 14 Jul 2020 08:02:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:02:48: #1 finished! INFO @ Tue, 14 Jul 2020 08:02:48: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:02:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:02:49: #2 number of paired peaks: 297 WARNING @ Tue, 14 Jul 2020 08:02:49: Fewer paired peaks (297) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 297 pairs to build model! INFO @ Tue, 14 Jul 2020 08:02:49: start model_add_line... INFO @ Tue, 14 Jul 2020 08:02:49: start X-correlation... INFO @ Tue, 14 Jul 2020 08:02:49: end of X-cor INFO @ Tue, 14 Jul 2020 08:02:49: #2 finished! INFO @ Tue, 14 Jul 2020 08:02:49: #2 predicted fragment length is 1 bps INFO @ Tue, 14 Jul 2020 08:02:49: #2 alternative fragment length(s) may be 1,31,552 bps INFO @ Tue, 14 Jul 2020 08:02:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7630549/SRX7630549.05_model.r WARNING @ Tue, 14 Jul 2020 08:02:49: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:02:49: #2 You may need to consider one of the other alternative d(s): 1,31,552 WARNING @ Tue, 14 Jul 2020 08:02:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 08:02:49: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:02:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:02:50: 11000000 INFO @ Tue, 14 Jul 2020 08:02:50: 5000000 INFO @ Tue, 14 Jul 2020 08:02:55: 12000000 INFO @ Tue, 14 Jul 2020 08:02:55: 6000000 INFO @ Tue, 14 Jul 2020 08:02:59: 13000000 INFO @ Tue, 14 Jul 2020 08:03:00: 7000000 INFO @ Tue, 14 Jul 2020 08:03:05: 14000000 INFO @ Tue, 14 Jul 2020 08:03:05: 8000000 INFO @ Tue, 14 Jul 2020 08:03:10: 15000000 INFO @ Tue, 14 Jul 2020 08:03:11: 9000000 INFO @ Tue, 14 Jul 2020 08:03:15: 16000000 INFO @ Tue, 14 Jul 2020 08:03:16: 10000000 INFO @ Tue, 14 Jul 2020 08:03:18: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:03:18: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 08:03:18: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 08:03:18: #1 total tags in treatment: 16765361 INFO @ Tue, 14 Jul 2020 08:03:18: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:03:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:03:19: #1 tags after filtering in treatment: 16765361 INFO @ Tue, 14 Jul 2020 08:03:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:03:19: #1 finished! INFO @ Tue, 14 Jul 2020 08:03:19: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:03:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:03:20: #2 number of paired peaks: 297 WARNING @ Tue, 14 Jul 2020 08:03:20: Fewer paired peaks (297) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 297 pairs to build model! INFO @ Tue, 14 Jul 2020 08:03:20: start model_add_line... INFO @ Tue, 14 Jul 2020 08:03:20: start X-correlation... INFO @ Tue, 14 Jul 2020 08:03:20: end of X-cor INFO @ Tue, 14 Jul 2020 08:03:20: #2 finished! INFO @ Tue, 14 Jul 2020 08:03:20: #2 predicted fragment length is 1 bps INFO @ Tue, 14 Jul 2020 08:03:20: #2 alternative fragment length(s) may be 1,31,552 bps INFO @ Tue, 14 Jul 2020 08:03:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7630549/SRX7630549.10_model.r WARNING @ Tue, 14 Jul 2020 08:03:20: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:03:20: #2 You may need to consider one of the other alternative d(s): 1,31,552 WARNING @ Tue, 14 Jul 2020 08:03:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 08:03:20: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:03:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:03:21: 11000000 INFO @ Tue, 14 Jul 2020 08:03:26: 12000000 INFO @ Tue, 14 Jul 2020 08:03:31: 13000000 INFO @ Tue, 14 Jul 2020 08:03:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7630549/SRX7630549.05_peaks.xls INFO @ Tue, 14 Jul 2020 08:03:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7630549/SRX7630549.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:03:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7630549/SRX7630549.05_summits.bed INFO @ Tue, 14 Jul 2020 08:03:32: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:03:36: 14000000 INFO @ Tue, 14 Jul 2020 08:03:41: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 08:03:46: 16000000 INFO @ Tue, 14 Jul 2020 08:03:50: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 08:03:50: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 08:03:50: #1 total tags in treatment: 16765361 INFO @ Tue, 14 Jul 2020 08:03:50: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:03:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:03:50: #1 tags after filtering in treatment: 16765361 INFO @ Tue, 14 Jul 2020 08:03:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:03:50: #1 finished! INFO @ Tue, 14 Jul 2020 08:03:50: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:03:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:03:50: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:03:51: #2 number of paired peaks: 297 WARNING @ Tue, 14 Jul 2020 08:03:51: Fewer paired peaks (297) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 297 pairs to build model! INFO @ Tue, 14 Jul 2020 08:03:51: start model_add_line... INFO @ Tue, 14 Jul 2020 08:03:52: start X-correlation... INFO @ Tue, 14 Jul 2020 08:03:52: end of X-cor INFO @ Tue, 14 Jul 2020 08:03:52: #2 finished! INFO @ Tue, 14 Jul 2020 08:03:52: #2 predicted fragment length is 1 bps INFO @ Tue, 14 Jul 2020 08:03:52: #2 alternative fragment length(s) may be 1,31,552 bps INFO @ Tue, 14 Jul 2020 08:03:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7630549/SRX7630549.20_model.r WARNING @ Tue, 14 Jul 2020 08:03:52: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:03:52: #2 You may need to consider one of the other alternative d(s): 1,31,552 WARNING @ Tue, 14 Jul 2020 08:03:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 08:03:52: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:03:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:04:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7630549/SRX7630549.10_peaks.xls INFO @ Tue, 14 Jul 2020 08:04:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7630549/SRX7630549.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:04:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7630549/SRX7630549.10_summits.bed INFO @ Tue, 14 Jul 2020 08:04:04: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:04:22: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 08:04:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7630549/SRX7630549.20_peaks.xls INFO @ Tue, 14 Jul 2020 08:04:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7630549/SRX7630549.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:04:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7630549/SRX7630549.20_summits.bed INFO @ Tue, 14 Jul 2020 08:04:36: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling