Job ID = 14160709 SRX = SRX10399022 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: 00:05:39 24779313 reads; of these: 24779313 (100.00%) were unpaired; of these: 440647 (1.78%) aligned 0 times 20182108 (81.45%) aligned exactly 1 time 4156558 (16.77%) aligned >1 times 98.22% overall alignment rate Time searching: 00:05:39 Overall time: 00:05:39 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] 2750555 / 24338666 = 0.1130 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 @ Thu, 09 Dec 2021 04:00:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10399022/SRX10399022.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10399022/SRX10399022.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10399022/SRX10399022.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10399022/SRX10399022.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, 09 Dec 2021 04:00:10: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:00:10: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:00:15: 1000000 INFO @ Thu, 09 Dec 2021 04:00:20: 2000000 INFO @ Thu, 09 Dec 2021 04:00:25: 3000000 INFO @ Thu, 09 Dec 2021 04:00:30: 4000000 INFO @ Thu, 09 Dec 2021 04:00:35: 5000000 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 @ Thu, 09 Dec 2021 04:00:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10399022/SRX10399022.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10399022/SRX10399022.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10399022/SRX10399022.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10399022/SRX10399022.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, 09 Dec 2021 04:00:40: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:00:40: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:00:40: 6000000 INFO @ Thu, 09 Dec 2021 04:00:45: 1000000 INFO @ Thu, 09 Dec 2021 04:00:46: 7000000 INFO @ Thu, 09 Dec 2021 04:00:51: 2000000 INFO @ Thu, 09 Dec 2021 04:00:51: 8000000 INFO @ Thu, 09 Dec 2021 04:00:56: 3000000 INFO @ Thu, 09 Dec 2021 04:00:57: 9000000 INFO @ Thu, 09 Dec 2021 04:01:02: 4000000 INFO @ Thu, 09 Dec 2021 04:01:02: 10000000 INFO @ Thu, 09 Dec 2021 04:01:07: 5000000 BedGraph に変換中... INFO @ Thu, 09 Dec 2021 04:01:08: 11000000 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 @ Thu, 09 Dec 2021 04:01:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10399022/SRX10399022.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10399022/SRX10399022.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10399022/SRX10399022.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10399022/SRX10399022.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, 09 Dec 2021 04:01:10: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:01:10: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:01:13: 6000000 INFO @ Thu, 09 Dec 2021 04:01:13: 12000000 INFO @ Thu, 09 Dec 2021 04:01:16: 1000000 INFO @ Thu, 09 Dec 2021 04:01:19: 7000000 INFO @ Thu, 09 Dec 2021 04:01:19: 13000000 INFO @ Thu, 09 Dec 2021 04:01:22: 2000000 INFO @ Thu, 09 Dec 2021 04:01:24: 8000000 INFO @ Thu, 09 Dec 2021 04:01:25: 14000000 INFO @ Thu, 09 Dec 2021 04:01:29: 3000000 INFO @ Thu, 09 Dec 2021 04:01:30: 9000000 INFO @ Thu, 09 Dec 2021 04:01:31: 15000000 INFO @ Thu, 09 Dec 2021 04:01:36: 4000000 INFO @ Thu, 09 Dec 2021 04:01:36: 10000000 INFO @ Thu, 09 Dec 2021 04:01:37: 16000000 INFO @ Thu, 09 Dec 2021 04:01:42: 11000000 INFO @ Thu, 09 Dec 2021 04:01:42: 5000000 INFO @ Thu, 09 Dec 2021 04:01:42: 17000000 INFO @ Thu, 09 Dec 2021 04:01:48: 12000000 INFO @ Thu, 09 Dec 2021 04:01:48: 18000000 INFO @ Thu, 09 Dec 2021 04:01:49: 6000000 INFO @ Thu, 09 Dec 2021 04:01:53: 13000000 INFO @ Thu, 09 Dec 2021 04:01:54: 19000000 INFO @ Thu, 09 Dec 2021 04:01:55: 7000000 INFO @ Thu, 09 Dec 2021 04:01:59: 14000000 INFO @ Thu, 09 Dec 2021 04:02:00: 20000000 INFO @ Thu, 09 Dec 2021 04:02:02: 8000000 INFO @ Thu, 09 Dec 2021 04:02:05: 15000000 INFO @ Thu, 09 Dec 2021 04:02:06: 21000000 INFO @ Thu, 09 Dec 2021 04:02:08: 9000000 INFO @ Thu, 09 Dec 2021 04:02:09: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 04:02:09: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 04:02:09: #1 total tags in treatment: 21588111 INFO @ Thu, 09 Dec 2021 04:02:09: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:02:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 04:02:09: #1 tags after filtering in treatment: 21588111 INFO @ Thu, 09 Dec 2021 04:02:09: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:02:09: #1 finished! INFO @ Thu, 09 Dec 2021 04:02:09: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:02:09: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:02:11: 16000000 INFO @ Thu, 09 Dec 2021 04:02:11: #2 number of paired peaks: 180 WARNING @ Thu, 09 Dec 2021 04:02:11: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Thu, 09 Dec 2021 04:02:11: start model_add_line... INFO @ Thu, 09 Dec 2021 04:02:11: start X-correlation... INFO @ Thu, 09 Dec 2021 04:02:11: end of X-cor INFO @ Thu, 09 Dec 2021 04:02:11: #2 finished! INFO @ Thu, 09 Dec 2021 04:02:11: #2 predicted fragment length is 1 bps INFO @ Thu, 09 Dec 2021 04:02:11: #2 alternative fragment length(s) may be 1,48,570 bps INFO @ Thu, 09 Dec 2021 04:02:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10399022/SRX10399022.05_model.r WARNING @ Thu, 09 Dec 2021 04:02:11: #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, 09 Dec 2021 04:02:11: #2 You may need to consider one of the other alternative d(s): 1,48,570 WARNING @ Thu, 09 Dec 2021 04:02:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 04:02:11: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:02:11: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:02:15: 10000000 INFO @ Thu, 09 Dec 2021 04:02:16: 17000000 INFO @ Thu, 09 Dec 2021 04:02:21: 11000000 INFO @ Thu, 09 Dec 2021 04:02:22: 18000000 INFO @ Thu, 09 Dec 2021 04:02:27: 12000000 INFO @ Thu, 09 Dec 2021 04:02:28: 19000000 INFO @ Thu, 09 Dec 2021 04:02:33: 20000000 INFO @ Thu, 09 Dec 2021 04:02:34: 13000000 INFO @ Thu, 09 Dec 2021 04:02:39: 21000000 INFO @ Thu, 09 Dec 2021 04:02:40: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 04:02:43: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 04:02:43: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 04:02:43: #1 total tags in treatment: 21588111 INFO @ Thu, 09 Dec 2021 04:02:43: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:02:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 04:02:43: #1 tags after filtering in treatment: 21588111 INFO @ Thu, 09 Dec 2021 04:02:43: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:02:43: #1 finished! INFO @ Thu, 09 Dec 2021 04:02:43: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:02:43: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:02:44: #2 number of paired peaks: 180 WARNING @ Thu, 09 Dec 2021 04:02:44: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Thu, 09 Dec 2021 04:02:44: start model_add_line... INFO @ Thu, 09 Dec 2021 04:02:45: start X-correlation... INFO @ Thu, 09 Dec 2021 04:02:45: end of X-cor INFO @ Thu, 09 Dec 2021 04:02:45: #2 finished! INFO @ Thu, 09 Dec 2021 04:02:45: #2 predicted fragment length is 1 bps INFO @ Thu, 09 Dec 2021 04:02:45: #2 alternative fragment length(s) may be 1,48,570 bps INFO @ Thu, 09 Dec 2021 04:02:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10399022/SRX10399022.10_model.r WARNING @ Thu, 09 Dec 2021 04:02:45: #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, 09 Dec 2021 04:02:45: #2 You may need to consider one of the other alternative d(s): 1,48,570 WARNING @ Thu, 09 Dec 2021 04:02:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 04:02:45: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:02:45: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:02:45: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:02:46: 15000000 INFO @ Thu, 09 Dec 2021 04:02:52: 16000000 INFO @ Thu, 09 Dec 2021 04:02:58: 17000000 INFO @ Thu, 09 Dec 2021 04:03:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10399022/SRX10399022.05_peaks.xls INFO @ Thu, 09 Dec 2021 04:03:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10399022/SRX10399022.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:03:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10399022/SRX10399022.05_summits.bed INFO @ Thu, 09 Dec 2021 04:03:01: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 04:03:04: 18000000 INFO @ Thu, 09 Dec 2021 04:03:10: 19000000 INFO @ Thu, 09 Dec 2021 04:03:17: 20000000 INFO @ Thu, 09 Dec 2021 04:03:18: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:03:23: 21000000 INFO @ Thu, 09 Dec 2021 04:03:26: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 04:03:26: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 04:03:26: #1 total tags in treatment: 21588111 INFO @ Thu, 09 Dec 2021 04:03:26: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:03:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 04:03:27: #1 tags after filtering in treatment: 21588111 INFO @ Thu, 09 Dec 2021 04:03:27: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:03:27: #1 finished! INFO @ Thu, 09 Dec 2021 04:03:27: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:03:27: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:03:28: #2 number of paired peaks: 180 WARNING @ Thu, 09 Dec 2021 04:03:28: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Thu, 09 Dec 2021 04:03:28: start model_add_line... INFO @ Thu, 09 Dec 2021 04:03:28: start X-correlation... INFO @ Thu, 09 Dec 2021 04:03:28: end of X-cor INFO @ Thu, 09 Dec 2021 04:03:28: #2 finished! INFO @ Thu, 09 Dec 2021 04:03:28: #2 predicted fragment length is 1 bps INFO @ Thu, 09 Dec 2021 04:03:28: #2 alternative fragment length(s) may be 1,48,570 bps INFO @ Thu, 09 Dec 2021 04:03:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10399022/SRX10399022.20_model.r WARNING @ Thu, 09 Dec 2021 04:03:28: #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, 09 Dec 2021 04:03:28: #2 You may need to consider one of the other alternative d(s): 1,48,570 WARNING @ Thu, 09 Dec 2021 04:03:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 04:03:28: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:03:28: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 04:03:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10399022/SRX10399022.10_peaks.xls INFO @ Thu, 09 Dec 2021 04:03:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10399022/SRX10399022.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:03:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10399022/SRX10399022.10_summits.bed INFO @ Thu, 09 Dec 2021 04:03:33: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 04:04:02: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:04:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10399022/SRX10399022.20_peaks.xls INFO @ Thu, 09 Dec 2021 04:04:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10399022/SRX10399022.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:04:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10399022/SRX10399022.20_summits.bed INFO @ Thu, 09 Dec 2021 04:04:18: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling