Job ID = 6508864 SRX = SRX495237 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T15:13:31 prefetch.2.10.7: 1) Downloading 'SRR1198742'... 2020-06-26T15:13:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T15:15:52 prefetch.2.10.7: HTTPS download succeed 2020-06-26T15:15:52 prefetch.2.10.7: 1) 'SRR1198742' was downloaded successfully Read 20636266 spots for SRR1198742/SRR1198742.sra Written 20636266 spots for SRR1198742/SRR1198742.sra 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: 00:08:06 20636266 reads; of these: 20636266 (100.00%) were unpaired; of these: 325879 (1.58%) aligned 0 times 14208441 (68.85%) aligned exactly 1 time 6101946 (29.57%) aligned >1 times 98.42% overall alignment rate Time searching: 00:08:06 Overall time: 00:08:06 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 4636506 / 20310387 = 0.2283 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, 27 Jun 2020 00:31:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495237/SRX495237.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495237/SRX495237.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495237/SRX495237.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495237/SRX495237.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 27 Jun 2020 00:31:06: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:31:06: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:31:11: 1000000 INFO @ Sat, 27 Jun 2020 00:31:16: 2000000 INFO @ Sat, 27 Jun 2020 00:31:21: 3000000 INFO @ Sat, 27 Jun 2020 00:31:26: 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 @ Sat, 27 Jun 2020 00:31:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495237/SRX495237.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495237/SRX495237.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495237/SRX495237.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495237/SRX495237.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 27 Jun 2020 00:31:29: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:31:29: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:31:31: 5000000 INFO @ Sat, 27 Jun 2020 00:31:35: 1000000 INFO @ Sat, 27 Jun 2020 00:31:37: 6000000 INFO @ Sat, 27 Jun 2020 00:31:40: 2000000 INFO @ Sat, 27 Jun 2020 00:31:42: 7000000 INFO @ Sat, 27 Jun 2020 00:31:45: 3000000 INFO @ Sat, 27 Jun 2020 00:31:47: 8000000 INFO @ Sat, 27 Jun 2020 00:31:50: 4000000 INFO @ Sat, 27 Jun 2020 00:31:52: 9000000 INFO @ Sat, 27 Jun 2020 00:31:55: 5000000 INFO @ Sat, 27 Jun 2020 00:31:57: 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 @ Sat, 27 Jun 2020 00:32:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495237/SRX495237.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495237/SRX495237.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495237/SRX495237.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495237/SRX495237.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 27 Jun 2020 00:32:00: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:32:00: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:32:01: 6000000 INFO @ Sat, 27 Jun 2020 00:32:02: 11000000 INFO @ Sat, 27 Jun 2020 00:32:07: 1000000 INFO @ Sat, 27 Jun 2020 00:32:07: 7000000 INFO @ Sat, 27 Jun 2020 00:32:07: 12000000 INFO @ Sat, 27 Jun 2020 00:32:12: 8000000 INFO @ Sat, 27 Jun 2020 00:32:13: 13000000 INFO @ Sat, 27 Jun 2020 00:32:15: 2000000 INFO @ Sat, 27 Jun 2020 00:32:18: 9000000 INFO @ Sat, 27 Jun 2020 00:32:18: 14000000 INFO @ Sat, 27 Jun 2020 00:32:21: 3000000 INFO @ Sat, 27 Jun 2020 00:32:23: 10000000 INFO @ Sat, 27 Jun 2020 00:32:24: 15000000 INFO @ Sat, 27 Jun 2020 00:32:28: 4000000 INFO @ Sat, 27 Jun 2020 00:32:29: 11000000 INFO @ Sat, 27 Jun 2020 00:32:29: #1 tag size is determined as 44 bps INFO @ Sat, 27 Jun 2020 00:32:29: #1 tag size = 44 INFO @ Sat, 27 Jun 2020 00:32:29: #1 total tags in treatment: 15673881 INFO @ Sat, 27 Jun 2020 00:32:29: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:32:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:32:29: #1 tags after filtering in treatment: 15673872 INFO @ Sat, 27 Jun 2020 00:32:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:32:29: #1 finished! INFO @ Sat, 27 Jun 2020 00:32:29: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:32:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:32:31: #2 number of paired peaks: 302 WARNING @ Sat, 27 Jun 2020 00:32:31: Fewer paired peaks (302) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 302 pairs to build model! INFO @ Sat, 27 Jun 2020 00:32:31: start model_add_line... INFO @ Sat, 27 Jun 2020 00:32:31: start X-correlation... INFO @ Sat, 27 Jun 2020 00:32:31: end of X-cor INFO @ Sat, 27 Jun 2020 00:32:31: #2 finished! INFO @ Sat, 27 Jun 2020 00:32:31: #2 predicted fragment length is 2 bps INFO @ Sat, 27 Jun 2020 00:32:31: #2 alternative fragment length(s) may be 2,43,505,536,578 bps INFO @ Sat, 27 Jun 2020 00:32:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495237/SRX495237.05_model.r WARNING @ Sat, 27 Jun 2020 00:32:31: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:32:31: #2 You may need to consider one of the other alternative d(s): 2,43,505,536,578 WARNING @ Sat, 27 Jun 2020 00:32:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:32:31: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:32:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:32:34: 5000000 INFO @ Sat, 27 Jun 2020 00:32:34: 12000000 INFO @ Sat, 27 Jun 2020 00:32:41: 13000000 INFO @ Sat, 27 Jun 2020 00:32:42: 6000000 INFO @ Sat, 27 Jun 2020 00:32:46: 14000000 INFO @ Sat, 27 Jun 2020 00:32:48: 7000000 INFO @ Sat, 27 Jun 2020 00:32:52: 15000000 INFO @ Sat, 27 Jun 2020 00:32:56: 8000000 INFO @ Sat, 27 Jun 2020 00:32:56: #1 tag size is determined as 44 bps INFO @ Sat, 27 Jun 2020 00:32:56: #1 tag size = 44 INFO @ Sat, 27 Jun 2020 00:32:56: #1 total tags in treatment: 15673881 INFO @ Sat, 27 Jun 2020 00:32:56: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:32:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:32:56: #1 tags after filtering in treatment: 15673872 INFO @ Sat, 27 Jun 2020 00:32:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:32:56: #1 finished! INFO @ Sat, 27 Jun 2020 00:32:56: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:32:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:32:57: #2 number of paired peaks: 302 WARNING @ Sat, 27 Jun 2020 00:32:57: Fewer paired peaks (302) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 302 pairs to build model! INFO @ Sat, 27 Jun 2020 00:32:57: start model_add_line... INFO @ Sat, 27 Jun 2020 00:32:57: start X-correlation... INFO @ Sat, 27 Jun 2020 00:32:57: end of X-cor INFO @ Sat, 27 Jun 2020 00:32:57: #2 finished! INFO @ Sat, 27 Jun 2020 00:32:57: #2 predicted fragment length is 2 bps INFO @ Sat, 27 Jun 2020 00:32:57: #2 alternative fragment length(s) may be 2,43,505,536,578 bps INFO @ Sat, 27 Jun 2020 00:32:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495237/SRX495237.10_model.r WARNING @ Sat, 27 Jun 2020 00:32:58: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:32:58: #2 You may need to consider one of the other alternative d(s): 2,43,505,536,578 WARNING @ Sat, 27 Jun 2020 00:32:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:32:58: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:32:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:33:00: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:33:02: 9000000 INFO @ Sat, 27 Jun 2020 00:33:08: 10000000 INFO @ Sat, 27 Jun 2020 00:33:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495237/SRX495237.05_peaks.xls INFO @ Sat, 27 Jun 2020 00:33:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495237/SRX495237.05_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:33:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495237/SRX495237.05_summits.bed INFO @ Sat, 27 Jun 2020 00:33:14: Done! INFO @ Sat, 27 Jun 2020 00:33:14: 11000000 pass1 - making usageList (0 chroms): 40 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:33:21: 12000000 INFO @ Sat, 27 Jun 2020 00:33:25: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:33:28: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 27 Jun 2020 00:33:34: 14000000 INFO @ Sat, 27 Jun 2020 00:33:39: 15000000 INFO @ Sat, 27 Jun 2020 00:33:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495237/SRX495237.10_peaks.xls INFO @ Sat, 27 Jun 2020 00:33:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495237/SRX495237.10_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:33:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495237/SRX495237.10_summits.bed INFO @ Sat, 27 Jun 2020 00:33:41: Done! pass1 - making usageList (0 chroms): 42 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:33:44: #1 tag size is determined as 44 bps INFO @ Sat, 27 Jun 2020 00:33:44: #1 tag size = 44 INFO @ Sat, 27 Jun 2020 00:33:44: #1 total tags in treatment: 15673881 INFO @ Sat, 27 Jun 2020 00:33:44: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:33:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:33:44: #1 tags after filtering in treatment: 15673872 INFO @ Sat, 27 Jun 2020 00:33:44: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:33:44: #1 finished! INFO @ Sat, 27 Jun 2020 00:33:44: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:33:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:33:45: #2 number of paired peaks: 302 WARNING @ Sat, 27 Jun 2020 00:33:45: Fewer paired peaks (302) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 302 pairs to build model! INFO @ Sat, 27 Jun 2020 00:33:45: start model_add_line... INFO @ Sat, 27 Jun 2020 00:33:46: start X-correlation... INFO @ Sat, 27 Jun 2020 00:33:46: end of X-cor INFO @ Sat, 27 Jun 2020 00:33:46: #2 finished! INFO @ Sat, 27 Jun 2020 00:33:46: #2 predicted fragment length is 2 bps INFO @ Sat, 27 Jun 2020 00:33:46: #2 alternative fragment length(s) may be 2,43,505,536,578 bps INFO @ Sat, 27 Jun 2020 00:33:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495237/SRX495237.20_model.r WARNING @ Sat, 27 Jun 2020 00:33:46: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:33:46: #2 You may need to consider one of the other alternative d(s): 2,43,505,536,578 WARNING @ Sat, 27 Jun 2020 00:33:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:33:46: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:33:46: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 27 Jun 2020 00:34:16: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:34:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495237/SRX495237.20_peaks.xls INFO @ Sat, 27 Jun 2020 00:34:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495237/SRX495237.20_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:34:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495237/SRX495237.20_summits.bed INFO @ Sat, 27 Jun 2020 00:34:32: Done! pass1 - making usageList (0 chroms): 46 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling