Job ID = 6458553 SRX = SRX5343088 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:34:49 prefetch.2.10.7: 1) Downloading 'SRR8540865'... 2020-06-21T12:34:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:37:16 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:37:16 prefetch.2.10.7: 1) 'SRR8540865' was downloaded successfully 2020-06-21T12:37:16 prefetch.2.10.7: 'SRR8540865' has 0 unresolved dependencies Read 21093525 spots for SRR8540865/SRR8540865.sra Written 21093525 spots for SRR8540865/SRR8540865.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: 00:07:56 21093525 reads; of these: 21093525 (100.00%) were unpaired; of these: 1045375 (4.96%) aligned 0 times 13959472 (66.18%) aligned exactly 1 time 6088678 (28.87%) aligned >1 times 95.04% overall alignment rate Time searching: 00:07:56 Overall time: 00:07:56 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] 2875993 / 20048150 = 0.1435 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 21:52:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343088/SRX5343088.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343088/SRX5343088.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343088/SRX5343088.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343088/SRX5343088.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 21:52:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:52:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:52:40: 1000000 INFO @ Sun, 21 Jun 2020 21:52:45: 2000000 INFO @ Sun, 21 Jun 2020 21:52:50: 3000000 INFO @ Sun, 21 Jun 2020 21:52:55: 4000000 INFO @ Sun, 21 Jun 2020 21:53:00: 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 21:53:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343088/SRX5343088.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343088/SRX5343088.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343088/SRX5343088.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343088/SRX5343088.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 21:53:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:53:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:53:05: 6000000 INFO @ Sun, 21 Jun 2020 21:53:10: 7000000 INFO @ Sun, 21 Jun 2020 21:53:10: 1000000 INFO @ Sun, 21 Jun 2020 21:53:16: 8000000 INFO @ Sun, 21 Jun 2020 21:53:16: 2000000 INFO @ Sun, 21 Jun 2020 21:53:21: 9000000 INFO @ Sun, 21 Jun 2020 21:53:21: 3000000 INFO @ Sun, 21 Jun 2020 21:53:26: 10000000 INFO @ Sun, 21 Jun 2020 21:53:27: 4000000 INFO @ Sun, 21 Jun 2020 21:53:31: 11000000 INFO @ Sun, 21 Jun 2020 21:53:32: 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 @ Sun, 21 Jun 2020 21:53:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343088/SRX5343088.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343088/SRX5343088.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343088/SRX5343088.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343088/SRX5343088.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 21:53:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:53:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:53:36: 12000000 INFO @ Sun, 21 Jun 2020 21:53:38: 6000000 INFO @ Sun, 21 Jun 2020 21:53:41: 1000000 INFO @ Sun, 21 Jun 2020 21:53:41: 13000000 INFO @ Sun, 21 Jun 2020 21:53:43: 7000000 INFO @ Sun, 21 Jun 2020 21:53:46: 2000000 INFO @ Sun, 21 Jun 2020 21:53:46: 14000000 INFO @ Sun, 21 Jun 2020 21:53:49: 8000000 INFO @ Sun, 21 Jun 2020 21:53:51: 3000000 INFO @ Sun, 21 Jun 2020 21:53:52: 15000000 INFO @ Sun, 21 Jun 2020 21:53:54: 9000000 INFO @ Sun, 21 Jun 2020 21:53:56: 4000000 INFO @ Sun, 21 Jun 2020 21:53:57: 16000000 INFO @ Sun, 21 Jun 2020 21:54:00: 10000000 INFO @ Sun, 21 Jun 2020 21:54:02: 5000000 INFO @ Sun, 21 Jun 2020 21:54:02: 17000000 INFO @ Sun, 21 Jun 2020 21:54:03: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:54:03: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:54:03: #1 total tags in treatment: 17172157 INFO @ Sun, 21 Jun 2020 21:54:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:54:03: #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 21:54:04: #1 tags after filtering in treatment: 17172156 INFO @ Sun, 21 Jun 2020 21:54:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:54:04: #1 finished! INFO @ Sun, 21 Jun 2020 21:54:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:54:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:54:05: #2 number of paired peaks: 281 WARNING @ Sun, 21 Jun 2020 21:54:05: Fewer paired peaks (281) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 281 pairs to build model! INFO @ Sun, 21 Jun 2020 21:54:05: start model_add_line... INFO @ Sun, 21 Jun 2020 21:54:05: start X-correlation... INFO @ Sun, 21 Jun 2020 21:54:05: end of X-cor INFO @ Sun, 21 Jun 2020 21:54:05: #2 finished! INFO @ Sun, 21 Jun 2020 21:54:05: #2 predicted fragment length is 59 bps INFO @ Sun, 21 Jun 2020 21:54:05: #2 alternative fragment length(s) may be 3,59,564 bps INFO @ Sun, 21 Jun 2020 21:54:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343088/SRX5343088.05_model.r WARNING @ Sun, 21 Jun 2020 21:54:05: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:54:05: #2 You may need to consider one of the other alternative d(s): 3,59,564 WARNING @ Sun, 21 Jun 2020 21:54:05: #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 21:54:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:54:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:54:05: 11000000 INFO @ Sun, 21 Jun 2020 21:54:07: 6000000 INFO @ Sun, 21 Jun 2020 21:54:11: 12000000 INFO @ Sun, 21 Jun 2020 21:54:12: 7000000 INFO @ Sun, 21 Jun 2020 21:54:16: 13000000 INFO @ Sun, 21 Jun 2020 21:54:18: 8000000 INFO @ Sun, 21 Jun 2020 21:54:22: 14000000 INFO @ Sun, 21 Jun 2020 21:54:23: 9000000 INFO @ Sun, 21 Jun 2020 21:54:28: 15000000 INFO @ Sun, 21 Jun 2020 21:54:28: 10000000 INFO @ Sun, 21 Jun 2020 21:54:33: 16000000 INFO @ Sun, 21 Jun 2020 21:54:34: 11000000 INFO @ Sun, 21 Jun 2020 21:54:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:54:39: 12000000 INFO @ Sun, 21 Jun 2020 21:54:39: 17000000 INFO @ Sun, 21 Jun 2020 21:54:40: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:54:40: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:54:40: #1 total tags in treatment: 17172157 INFO @ Sun, 21 Jun 2020 21:54:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:54:40: #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 21:54:41: #1 tags after filtering in treatment: 17172156 INFO @ Sun, 21 Jun 2020 21:54:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:54:41: #1 finished! INFO @ Sun, 21 Jun 2020 21:54:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:54:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:54:42: #2 number of paired peaks: 281 WARNING @ Sun, 21 Jun 2020 21:54:42: Fewer paired peaks (281) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 281 pairs to build model! INFO @ Sun, 21 Jun 2020 21:54:42: start model_add_line... INFO @ Sun, 21 Jun 2020 21:54:42: start X-correlation... INFO @ Sun, 21 Jun 2020 21:54:42: end of X-cor INFO @ Sun, 21 Jun 2020 21:54:42: #2 finished! INFO @ Sun, 21 Jun 2020 21:54:42: #2 predicted fragment length is 59 bps INFO @ Sun, 21 Jun 2020 21:54:42: #2 alternative fragment length(s) may be 3,59,564 bps INFO @ Sun, 21 Jun 2020 21:54:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343088/SRX5343088.10_model.r WARNING @ Sun, 21 Jun 2020 21:54:42: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:54:42: #2 You may need to consider one of the other alternative d(s): 3,59,564 WARNING @ Sun, 21 Jun 2020 21:54:42: #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 21:54:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:54:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:54:44: 13000000 INFO @ Sun, 21 Jun 2020 21:54:50: 14000000 INFO @ Sun, 21 Jun 2020 21:54:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343088/SRX5343088.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:54:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343088/SRX5343088.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:54:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343088/SRX5343088.05_summits.bed INFO @ Sun, 21 Jun 2020 21:54:53: Done! pass1 - making usageList (714 chroms): 1 millis pass2 - checking and writing primary data (2290 records, 4 fields): 20 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:54:55: 15000000 INFO @ Sun, 21 Jun 2020 21:55:01: 16000000 INFO @ Sun, 21 Jun 2020 21:55:06: 17000000 INFO @ Sun, 21 Jun 2020 21:55:07: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:55:07: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:55:07: #1 total tags in treatment: 17172157 INFO @ Sun, 21 Jun 2020 21:55:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:55:07: #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 21:55:08: #1 tags after filtering in treatment: 17172156 INFO @ Sun, 21 Jun 2020 21:55:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:55:08: #1 finished! INFO @ Sun, 21 Jun 2020 21:55:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:55:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:55:09: #2 number of paired peaks: 281 WARNING @ Sun, 21 Jun 2020 21:55:09: Fewer paired peaks (281) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 281 pairs to build model! INFO @ Sun, 21 Jun 2020 21:55:09: start model_add_line... INFO @ Sun, 21 Jun 2020 21:55:09: start X-correlation... INFO @ Sun, 21 Jun 2020 21:55:09: end of X-cor INFO @ Sun, 21 Jun 2020 21:55:09: #2 finished! INFO @ Sun, 21 Jun 2020 21:55:09: #2 predicted fragment length is 59 bps INFO @ Sun, 21 Jun 2020 21:55:09: #2 alternative fragment length(s) may be 3,59,564 bps INFO @ Sun, 21 Jun 2020 21:55:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343088/SRX5343088.20_model.r WARNING @ Sun, 21 Jun 2020 21:55:09: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:55:09: #2 You may need to consider one of the other alternative d(s): 3,59,564 WARNING @ Sun, 21 Jun 2020 21:55:09: #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 21:55:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:55:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:55:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:55:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343088/SRX5343088.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:55:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343088/SRX5343088.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:55:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343088/SRX5343088.10_summits.bed INFO @ Sun, 21 Jun 2020 21:55:32: Done! pass1 - making usageList (527 chroms): 1 millis pass2 - checking and writing primary data (1501 records, 4 fields): 56 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:55:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:56:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343088/SRX5343088.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:56:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343088/SRX5343088.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:56:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343088/SRX5343088.20_summits.bed INFO @ Sun, 21 Jun 2020 21:56:00: Done! pass1 - making usageList (309 chroms): 1 millis pass2 - checking and writing primary data (627 records, 4 fields): 9 millis CompletedMACS2peakCalling