Job ID = 6455002 SRX = SRX2618548 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:37:10 prefetch.2.10.7: 1) Downloading 'SRR5319102'... 2020-06-21T09:37:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:39:42 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:39:43 prefetch.2.10.7: 'SRR5319102' is valid 2020-06-21T09:39:43 prefetch.2.10.7: 1) 'SRR5319102' was downloaded successfully 2020-06-21T09:39:43 prefetch.2.10.7: 'SRR5319102' has 0 unresolved dependencies Read 22628889 spots for SRR5319102/SRR5319102.sra Written 22628889 spots for SRR5319102/SRR5319102.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: 00:06:37 22628889 reads; of these: 22628889 (100.00%) were unpaired; of these: 1001693 (4.43%) aligned 0 times 14374621 (63.52%) aligned exactly 1 time 7252575 (32.05%) aligned >1 times 95.57% overall alignment rate Time searching: 00:06:37 Overall time: 00:06:37 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 12 files... [bam_rmdupse_core] 3775200 / 21627196 = 0.1746 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 @ Sun, 21 Jun 2020 18:52:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618548/SRX2618548.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618548/SRX2618548.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618548/SRX2618548.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618548/SRX2618548.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 @ Sun, 21 Jun 2020 18:52:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:52:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:52:25: 1000000 INFO @ Sun, 21 Jun 2020 18:52:30: 2000000 INFO @ Sun, 21 Jun 2020 18:52:36: 3000000 INFO @ Sun, 21 Jun 2020 18:52:41: 4000000 INFO @ Sun, 21 Jun 2020 18:52:46: 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 @ Sun, 21 Jun 2020 18:52:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618548/SRX2618548.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618548/SRX2618548.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618548/SRX2618548.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618548/SRX2618548.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 @ Sun, 21 Jun 2020 18:52:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:52:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:52:52: 6000000 INFO @ Sun, 21 Jun 2020 18:52:55: 1000000 INFO @ Sun, 21 Jun 2020 18:52:58: 7000000 INFO @ Sun, 21 Jun 2020 18:53:01: 2000000 INFO @ Sun, 21 Jun 2020 18:53:04: 8000000 INFO @ Sun, 21 Jun 2020 18:53:07: 3000000 INFO @ Sun, 21 Jun 2020 18:53:10: 9000000 INFO @ Sun, 21 Jun 2020 18:53:13: 4000000 INFO @ Sun, 21 Jun 2020 18:53:16: 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 @ Sun, 21 Jun 2020 18:53:19: 5000000 INFO @ Sun, 21 Jun 2020 18:53:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618548/SRX2618548.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618548/SRX2618548.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618548/SRX2618548.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618548/SRX2618548.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 @ Sun, 21 Jun 2020 18:53:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:53:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:53:22: 11000000 INFO @ Sun, 21 Jun 2020 18:53:25: 6000000 INFO @ Sun, 21 Jun 2020 18:53:25: 1000000 INFO @ Sun, 21 Jun 2020 18:53:28: 12000000 INFO @ Sun, 21 Jun 2020 18:53:31: 7000000 INFO @ Sun, 21 Jun 2020 18:53:31: 2000000 INFO @ Sun, 21 Jun 2020 18:53:33: 13000000 INFO @ Sun, 21 Jun 2020 18:53:37: 8000000 INFO @ Sun, 21 Jun 2020 18:53:37: 3000000 INFO @ Sun, 21 Jun 2020 18:53:40: 14000000 INFO @ Sun, 21 Jun 2020 18:53:42: 9000000 INFO @ Sun, 21 Jun 2020 18:53:43: 4000000 INFO @ Sun, 21 Jun 2020 18:53:46: 15000000 INFO @ Sun, 21 Jun 2020 18:53:48: 10000000 INFO @ Sun, 21 Jun 2020 18:53:49: 5000000 INFO @ Sun, 21 Jun 2020 18:53:52: 16000000 INFO @ Sun, 21 Jun 2020 18:53:54: 11000000 INFO @ Sun, 21 Jun 2020 18:53:55: 6000000 INFO @ Sun, 21 Jun 2020 18:53:58: 17000000 INFO @ Sun, 21 Jun 2020 18:54:00: 12000000 INFO @ Sun, 21 Jun 2020 18:54:01: 7000000 INFO @ Sun, 21 Jun 2020 18:54:03: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:54:03: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:54:03: #1 total tags in treatment: 17851996 INFO @ Sun, 21 Jun 2020 18:54:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:54:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:54:04: #1 tags after filtering in treatment: 17851996 INFO @ Sun, 21 Jun 2020 18:54:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:54:04: #1 finished! INFO @ Sun, 21 Jun 2020 18:54:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:54:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:54:05: #2 number of paired peaks: 855 WARNING @ Sun, 21 Jun 2020 18:54:05: Fewer paired peaks (855) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 855 pairs to build model! INFO @ Sun, 21 Jun 2020 18:54:05: start model_add_line... INFO @ Sun, 21 Jun 2020 18:54:05: start X-correlation... INFO @ Sun, 21 Jun 2020 18:54:05: end of X-cor INFO @ Sun, 21 Jun 2020 18:54:05: #2 finished! INFO @ Sun, 21 Jun 2020 18:54:05: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 18:54:05: #2 alternative fragment length(s) may be 2,21 bps INFO @ Sun, 21 Jun 2020 18:54:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618548/SRX2618548.05_model.r WARNING @ Sun, 21 Jun 2020 18:54:05: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:54:05: #2 You may need to consider one of the other alternative d(s): 2,21 WARNING @ Sun, 21 Jun 2020 18:54:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:54:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:54:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:54:06: 13000000 INFO @ Sun, 21 Jun 2020 18:54:07: 8000000 INFO @ Sun, 21 Jun 2020 18:54:12: 14000000 INFO @ Sun, 21 Jun 2020 18:54:12: 9000000 INFO @ Sun, 21 Jun 2020 18:54:18: 15000000 INFO @ Sun, 21 Jun 2020 18:54:18: 10000000 INFO @ Sun, 21 Jun 2020 18:54:24: 16000000 INFO @ Sun, 21 Jun 2020 18:54:24: 11000000 INFO @ Sun, 21 Jun 2020 18:54:30: 17000000 INFO @ Sun, 21 Jun 2020 18:54:30: 12000000 INFO @ Sun, 21 Jun 2020 18:54:35: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:54:35: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:54:35: #1 total tags in treatment: 17851996 INFO @ Sun, 21 Jun 2020 18:54:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:54:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:54:35: #1 tags after filtering in treatment: 17851996 INFO @ Sun, 21 Jun 2020 18:54:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:54:35: #1 finished! INFO @ Sun, 21 Jun 2020 18:54:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:54:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:54:36: 13000000 INFO @ Sun, 21 Jun 2020 18:54:36: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:54:37: #2 number of paired peaks: 855 WARNING @ Sun, 21 Jun 2020 18:54:37: Fewer paired peaks (855) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 855 pairs to build model! INFO @ Sun, 21 Jun 2020 18:54:37: start model_add_line... INFO @ Sun, 21 Jun 2020 18:54:37: start X-correlation... INFO @ Sun, 21 Jun 2020 18:54:37: end of X-cor INFO @ Sun, 21 Jun 2020 18:54:37: #2 finished! INFO @ Sun, 21 Jun 2020 18:54:37: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 18:54:37: #2 alternative fragment length(s) may be 2,21 bps INFO @ Sun, 21 Jun 2020 18:54:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618548/SRX2618548.10_model.r WARNING @ Sun, 21 Jun 2020 18:54:37: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:54:37: #2 You may need to consider one of the other alternative d(s): 2,21 WARNING @ Sun, 21 Jun 2020 18:54:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:54:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:54:37: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:54:42: 14000000 INFO @ Sun, 21 Jun 2020 18:54:47: 15000000 INFO @ Sun, 21 Jun 2020 18:54:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618548/SRX2618548.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:54:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618548/SRX2618548.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:54:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618548/SRX2618548.05_summits.bed INFO @ Sun, 21 Jun 2020 18:54:51: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:54:52: 16000000 INFO @ Sun, 21 Jun 2020 18:54:58: 17000000 INFO @ Sun, 21 Jun 2020 18:55:03: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:55:03: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:55:03: #1 total tags in treatment: 17851996 INFO @ Sun, 21 Jun 2020 18:55:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:55:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:55:03: #1 tags after filtering in treatment: 17851996 INFO @ Sun, 21 Jun 2020 18:55:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:55:03: #1 finished! INFO @ Sun, 21 Jun 2020 18:55:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:55:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:55:04: #2 number of paired peaks: 855 WARNING @ Sun, 21 Jun 2020 18:55:04: Fewer paired peaks (855) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 855 pairs to build model! INFO @ Sun, 21 Jun 2020 18:55:04: start model_add_line... INFO @ Sun, 21 Jun 2020 18:55:04: start X-correlation... INFO @ Sun, 21 Jun 2020 18:55:04: end of X-cor INFO @ Sun, 21 Jun 2020 18:55:04: #2 finished! INFO @ Sun, 21 Jun 2020 18:55:04: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 18:55:04: #2 alternative fragment length(s) may be 2,21 bps INFO @ Sun, 21 Jun 2020 18:55:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618548/SRX2618548.20_model.r WARNING @ Sun, 21 Jun 2020 18:55:04: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:55:04: #2 You may need to consider one of the other alternative d(s): 2,21 WARNING @ Sun, 21 Jun 2020 18:55:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:55:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:55:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:55:08: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:55:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618548/SRX2618548.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:55:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618548/SRX2618548.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:55:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618548/SRX2618548.10_summits.bed INFO @ Sun, 21 Jun 2020 18:55:22: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:55:36: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:55:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618548/SRX2618548.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:55:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618548/SRX2618548.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:55:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618548/SRX2618548.20_summits.bed INFO @ Sun, 21 Jun 2020 18:55:51: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling