Job ID = 6455887 SRX = SRX3020551 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:34:11 prefetch.2.10.7: 1) Downloading 'SRR5850464'... 2020-06-21T10:34:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:34:53 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:34:53 prefetch.2.10.7: 'SRR5850464' is valid 2020-06-21T10:34:53 prefetch.2.10.7: 1) 'SRR5850464' was downloaded successfully 2020-06-21T10:34:53 prefetch.2.10.7: 'SRR5850464' has 0 unresolved dependencies Read 6413143 spots for SRR5850464/SRR5850464.sra Written 6413143 spots for SRR5850464/SRR5850464.sra 2020-06-21T10:35:29 prefetch.2.10.7: 1) Downloading 'SRR5850465'... 2020-06-21T10:35:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:36:13 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:36:13 prefetch.2.10.7: 'SRR5850465' is valid 2020-06-21T10:36:13 prefetch.2.10.7: 1) 'SRR5850465' was downloaded successfully 2020-06-21T10:36:13 prefetch.2.10.7: 'SRR5850465' has 0 unresolved dependencies Read 6326047 spots for SRR5850465/SRR5850465.sra Written 6326047 spots for SRR5850465/SRR5850465.sra 2020-06-21T10:36:49 prefetch.2.10.7: 1) Downloading 'SRR5850466'... 2020-06-21T10:36:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:37:24 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:37:25 prefetch.2.10.7: 'SRR5850466' is valid 2020-06-21T10:37:25 prefetch.2.10.7: 1) 'SRR5850466' was downloaded successfully 2020-06-21T10:37:25 prefetch.2.10.7: 'SRR5850466' has 0 unresolved dependencies Read 6335611 spots for SRR5850466/SRR5850466.sra Written 6335611 spots for SRR5850466/SRR5850466.sra 2020-06-21T10:38:00 prefetch.2.10.7: 1) Downloading 'SRR5850467'... 2020-06-21T10:38:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:39:03 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:39:03 prefetch.2.10.7: 'SRR5850467' is valid 2020-06-21T10:39:03 prefetch.2.10.7: 1) 'SRR5850467' was downloaded successfully 2020-06-21T10:39:03 prefetch.2.10.7: 'SRR5850467' has 0 unresolved dependencies Read 6284885 spots for SRR5850467/SRR5850467.sra Written 6284885 spots for SRR5850467/SRR5850467.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: 00:07:44 25359686 reads; of these: 25359686 (100.00%) were unpaired; of these: 916816 (3.62%) aligned 0 times 16632810 (65.59%) aligned exactly 1 time 7810060 (30.80%) aligned >1 times 96.38% overall alignment rate Time searching: 00:07:44 Overall time: 00:07:44 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] 4746934 / 24442870 = 0.1942 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 19:53:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3020551/SRX3020551.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3020551/SRX3020551.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3020551/SRX3020551.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3020551/SRX3020551.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 19:53:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:53:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:54:00: 1000000 INFO @ Sun, 21 Jun 2020 19:54:05: 2000000 INFO @ Sun, 21 Jun 2020 19:54:10: 3000000 INFO @ Sun, 21 Jun 2020 19:54:15: 4000000 INFO @ Sun, 21 Jun 2020 19:54:20: 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 19:54:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3020551/SRX3020551.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3020551/SRX3020551.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3020551/SRX3020551.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3020551/SRX3020551.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 19:54:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:54:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:54:25: 6000000 INFO @ Sun, 21 Jun 2020 19:54:30: 1000000 INFO @ Sun, 21 Jun 2020 19:54:31: 7000000 INFO @ Sun, 21 Jun 2020 19:54:35: 2000000 INFO @ Sun, 21 Jun 2020 19:54:36: 8000000 INFO @ Sun, 21 Jun 2020 19:54:40: 3000000 INFO @ Sun, 21 Jun 2020 19:54:42: 9000000 INFO @ Sun, 21 Jun 2020 19:54:46: 4000000 INFO @ Sun, 21 Jun 2020 19:54:47: 10000000 INFO @ Sun, 21 Jun 2020 19:54:51: 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 19:54:52: 11000000 INFO @ Sun, 21 Jun 2020 19:54:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3020551/SRX3020551.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3020551/SRX3020551.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3020551/SRX3020551.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3020551/SRX3020551.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 19:54:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:54:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:54:57: 6000000 INFO @ Sun, 21 Jun 2020 19:54:58: 12000000 INFO @ Sun, 21 Jun 2020 19:55:01: 1000000 INFO @ Sun, 21 Jun 2020 19:55:02: 7000000 INFO @ Sun, 21 Jun 2020 19:55:03: 13000000 INFO @ Sun, 21 Jun 2020 19:55:07: 2000000 INFO @ Sun, 21 Jun 2020 19:55:08: 14000000 INFO @ Sun, 21 Jun 2020 19:55:08: 8000000 INFO @ Sun, 21 Jun 2020 19:55:13: 15000000 INFO @ Sun, 21 Jun 2020 19:55:13: 3000000 INFO @ Sun, 21 Jun 2020 19:55:14: 9000000 INFO @ Sun, 21 Jun 2020 19:55:18: 16000000 INFO @ Sun, 21 Jun 2020 19:55:20: 4000000 INFO @ Sun, 21 Jun 2020 19:55:20: 10000000 INFO @ Sun, 21 Jun 2020 19:55:25: 17000000 INFO @ Sun, 21 Jun 2020 19:55:26: 11000000 INFO @ Sun, 21 Jun 2020 19:55:26: 5000000 INFO @ Sun, 21 Jun 2020 19:55:30: 18000000 INFO @ Sun, 21 Jun 2020 19:55:32: 12000000 INFO @ Sun, 21 Jun 2020 19:55:32: 6000000 INFO @ Sun, 21 Jun 2020 19:55:35: 19000000 INFO @ Sun, 21 Jun 2020 19:55:37: 13000000 INFO @ Sun, 21 Jun 2020 19:55:39: 7000000 INFO @ Sun, 21 Jun 2020 19:55:39: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:55:39: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:55:39: #1 total tags in treatment: 19695936 INFO @ Sun, 21 Jun 2020 19:55:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:55:39: #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 19:55:40: #1 tags after filtering in treatment: 19695872 INFO @ Sun, 21 Jun 2020 19:55:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:55:40: #1 finished! INFO @ Sun, 21 Jun 2020 19:55:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:55:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:55:42: #2 number of paired peaks: 643 WARNING @ Sun, 21 Jun 2020 19:55:42: Fewer paired peaks (643) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 643 pairs to build model! INFO @ Sun, 21 Jun 2020 19:55:42: start model_add_line... INFO @ Sun, 21 Jun 2020 19:55:42: start X-correlation... INFO @ Sun, 21 Jun 2020 19:55:42: end of X-cor INFO @ Sun, 21 Jun 2020 19:55:42: #2 finished! INFO @ Sun, 21 Jun 2020 19:55:42: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 19:55:42: #2 alternative fragment length(s) may be 2,46 bps INFO @ Sun, 21 Jun 2020 19:55:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3020551/SRX3020551.05_model.r WARNING @ Sun, 21 Jun 2020 19:55:42: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:55:42: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Sun, 21 Jun 2020 19:55:42: #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 19:55:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:55:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:55:43: 14000000 INFO @ Sun, 21 Jun 2020 19:55:45: 8000000 INFO @ Sun, 21 Jun 2020 19:55:49: 15000000 INFO @ Sun, 21 Jun 2020 19:55:50: 9000000 INFO @ Sun, 21 Jun 2020 19:55:54: 16000000 INFO @ Sun, 21 Jun 2020 19:55:56: 10000000 INFO @ Sun, 21 Jun 2020 19:56:01: 17000000 INFO @ Sun, 21 Jun 2020 19:56:01: 11000000 INFO @ Sun, 21 Jun 2020 19:56:07: 18000000 INFO @ Sun, 21 Jun 2020 19:56:07: 12000000 INFO @ Sun, 21 Jun 2020 19:56:13: 19000000 INFO @ Sun, 21 Jun 2020 19:56:13: 13000000 INFO @ Sun, 21 Jun 2020 19:56:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:56:17: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:56:17: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:56:17: #1 total tags in treatment: 19695936 INFO @ Sun, 21 Jun 2020 19:56:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:56:17: #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 19:56:18: #1 tags after filtering in treatment: 19695872 INFO @ Sun, 21 Jun 2020 19:56:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:56:18: #1 finished! INFO @ Sun, 21 Jun 2020 19:56:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:56:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:56:18: 14000000 INFO @ Sun, 21 Jun 2020 19:56:19: #2 number of paired peaks: 643 WARNING @ Sun, 21 Jun 2020 19:56:19: Fewer paired peaks (643) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 643 pairs to build model! INFO @ Sun, 21 Jun 2020 19:56:19: start model_add_line... INFO @ Sun, 21 Jun 2020 19:56:20: start X-correlation... INFO @ Sun, 21 Jun 2020 19:56:20: end of X-cor INFO @ Sun, 21 Jun 2020 19:56:20: #2 finished! INFO @ Sun, 21 Jun 2020 19:56:20: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 19:56:20: #2 alternative fragment length(s) may be 2,46 bps INFO @ Sun, 21 Jun 2020 19:56:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3020551/SRX3020551.10_model.r WARNING @ Sun, 21 Jun 2020 19:56:20: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:56:20: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Sun, 21 Jun 2020 19:56:20: #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 19:56:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:56:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:56:23: 15000000 INFO @ Sun, 21 Jun 2020 19:56:29: 16000000 INFO @ Sun, 21 Jun 2020 19:56:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3020551/SRX3020551.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:56:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3020551/SRX3020551.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:56:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3020551/SRX3020551.05_summits.bed INFO @ Sun, 21 Jun 2020 19:56:31: Done! pass1 - making usageList (664 chroms): 1 millis pass2 - checking and writing primary data (3103 records, 4 fields): 40 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:56:35: 17000000 INFO @ Sun, 21 Jun 2020 19:56:40: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:56:46: 19000000 INFO @ Sun, 21 Jun 2020 19:56:50: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:56:50: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:56:50: #1 total tags in treatment: 19695936 INFO @ Sun, 21 Jun 2020 19:56:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:56:50: #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 19:56:51: #1 tags after filtering in treatment: 19695872 INFO @ Sun, 21 Jun 2020 19:56:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:56:51: #1 finished! INFO @ Sun, 21 Jun 2020 19:56:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:56:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:56:52: #2 number of paired peaks: 643 WARNING @ Sun, 21 Jun 2020 19:56:52: Fewer paired peaks (643) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 643 pairs to build model! INFO @ Sun, 21 Jun 2020 19:56:52: start model_add_line... INFO @ Sun, 21 Jun 2020 19:56:52: start X-correlation... INFO @ Sun, 21 Jun 2020 19:56:52: end of X-cor INFO @ Sun, 21 Jun 2020 19:56:52: #2 finished! INFO @ Sun, 21 Jun 2020 19:56:52: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 19:56:52: #2 alternative fragment length(s) may be 2,46 bps INFO @ Sun, 21 Jun 2020 19:56:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3020551/SRX3020551.20_model.r WARNING @ Sun, 21 Jun 2020 19:56:52: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:56:52: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Sun, 21 Jun 2020 19:56:52: #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 19:56:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:56:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:56:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:57:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3020551/SRX3020551.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:57:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3020551/SRX3020551.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:57:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3020551/SRX3020551.10_summits.bed INFO @ Sun, 21 Jun 2020 19:57:11: Done! pass1 - making usageList (533 chroms): 2 millis pass2 - checking and writing primary data (2023 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:57:26: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:57:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3020551/SRX3020551.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:57:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3020551/SRX3020551.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:57:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3020551/SRX3020551.20_summits.bed INFO @ Sun, 21 Jun 2020 19:57:43: Done! pass1 - making usageList (327 chroms): 2 millis pass2 - checking and writing primary data (748 records, 4 fields): 18 millis CompletedMACS2peakCalling