Job ID = 6456807 SRX = SRX3981698 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:06:24 prefetch.2.10.7: 1) Downloading 'SRR7050487'... 2020-06-21T11:06:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:07:19 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:07:19 prefetch.2.10.7: 'SRR7050487' is valid 2020-06-21T11:07:19 prefetch.2.10.7: 1) 'SRR7050487' was downloaded successfully 2020-06-21T11:07:19 prefetch.2.10.7: 'SRR7050487' has 0 unresolved dependencies Read 8149060 spots for SRR7050487/SRR7050487.sra Written 8149060 spots for SRR7050487/SRR7050487.sra 2020-06-21T11:07:54 prefetch.2.10.7: 1) Downloading 'SRR7050488'... 2020-06-21T11:07:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:08:30 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:08:30 prefetch.2.10.7: 'SRR7050488' is valid 2020-06-21T11:08:30 prefetch.2.10.7: 1) 'SRR7050488' was downloaded successfully 2020-06-21T11:08:30 prefetch.2.10.7: 'SRR7050488' has 0 unresolved dependencies Read 8140446 spots for SRR7050488/SRR7050488.sra Written 8140446 spots for SRR7050488/SRR7050488.sra 2020-06-21T11:09:06 prefetch.2.10.7: 1) Downloading 'SRR7050489'... 2020-06-21T11:09:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:09:59 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:10:00 prefetch.2.10.7: 'SRR7050489' is valid 2020-06-21T11:10:00 prefetch.2.10.7: 1) 'SRR7050489' was downloaded successfully 2020-06-21T11:10:00 prefetch.2.10.7: 'SRR7050489' has 0 unresolved dependencies Read 8176922 spots for SRR7050489/SRR7050489.sra Written 8176922 spots for SRR7050489/SRR7050489.sra 2020-06-21T11:10:35 prefetch.2.10.7: 1) Downloading 'SRR7050490'... 2020-06-21T11:10:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:11:26 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:11:26 prefetch.2.10.7: 'SRR7050490' is valid 2020-06-21T11:11:26 prefetch.2.10.7: 1) 'SRR7050490' was downloaded successfully 2020-06-21T11:11:26 prefetch.2.10.7: 'SRR7050490' has 0 unresolved dependencies Read 8211088 spots for SRR7050490/SRR7050490.sra Written 8211088 spots for SRR7050490/SRR7050490.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: 00:08:10 32677516 reads; of these: 32677516 (100.00%) were unpaired; of these: 1288423 (3.94%) aligned 0 times 24285283 (74.32%) aligned exactly 1 time 7103810 (21.74%) aligned >1 times 96.06% overall alignment rate Time searching: 00:08:10 Overall time: 00:08:10 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 16 files... [bam_rmdupse_core] 4098303 / 31389093 = 0.1306 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 20:26:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981698/SRX3981698.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981698/SRX3981698.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981698/SRX3981698.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981698/SRX3981698.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 20:26:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:26:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:26:21: 1000000 INFO @ Sun, 21 Jun 2020 20:26:27: 2000000 INFO @ Sun, 21 Jun 2020 20:26:32: 3000000 INFO @ Sun, 21 Jun 2020 20:26:37: 4000000 INFO @ Sun, 21 Jun 2020 20:26:42: 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 20:26:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981698/SRX3981698.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981698/SRX3981698.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981698/SRX3981698.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981698/SRX3981698.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 20:26:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:26:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:26:48: 6000000 INFO @ Sun, 21 Jun 2020 20:26:52: 1000000 INFO @ Sun, 21 Jun 2020 20:26:54: 7000000 INFO @ Sun, 21 Jun 2020 20:26:58: 2000000 INFO @ Sun, 21 Jun 2020 20:26:59: 8000000 INFO @ Sun, 21 Jun 2020 20:27:03: 3000000 INFO @ Sun, 21 Jun 2020 20:27:05: 9000000 INFO @ Sun, 21 Jun 2020 20:27:09: 4000000 INFO @ Sun, 21 Jun 2020 20:27:11: 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 20:27:15: 5000000 INFO @ Sun, 21 Jun 2020 20:27:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981698/SRX3981698.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981698/SRX3981698.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981698/SRX3981698.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981698/SRX3981698.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 20:27:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:27:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:27:16: 11000000 INFO @ Sun, 21 Jun 2020 20:27:20: 6000000 INFO @ Sun, 21 Jun 2020 20:27:22: 1000000 INFO @ Sun, 21 Jun 2020 20:27:22: 12000000 INFO @ Sun, 21 Jun 2020 20:27:26: 7000000 INFO @ Sun, 21 Jun 2020 20:27:27: 2000000 INFO @ Sun, 21 Jun 2020 20:27:28: 13000000 INFO @ Sun, 21 Jun 2020 20:27:32: 8000000 INFO @ Sun, 21 Jun 2020 20:27:33: 3000000 INFO @ Sun, 21 Jun 2020 20:27:34: 14000000 INFO @ Sun, 21 Jun 2020 20:27:37: 9000000 INFO @ Sun, 21 Jun 2020 20:27:39: 4000000 INFO @ Sun, 21 Jun 2020 20:27:39: 15000000 INFO @ Sun, 21 Jun 2020 20:27:43: 10000000 INFO @ Sun, 21 Jun 2020 20:27:45: 5000000 INFO @ Sun, 21 Jun 2020 20:27:45: 16000000 INFO @ Sun, 21 Jun 2020 20:27:49: 11000000 INFO @ Sun, 21 Jun 2020 20:27:50: 6000000 INFO @ Sun, 21 Jun 2020 20:27:51: 17000000 INFO @ Sun, 21 Jun 2020 20:27:54: 12000000 INFO @ Sun, 21 Jun 2020 20:27:56: 7000000 INFO @ Sun, 21 Jun 2020 20:27:57: 18000000 INFO @ Sun, 21 Jun 2020 20:28:00: 13000000 INFO @ Sun, 21 Jun 2020 20:28:02: 8000000 INFO @ Sun, 21 Jun 2020 20:28:02: 19000000 INFO @ Sun, 21 Jun 2020 20:28:06: 14000000 INFO @ Sun, 21 Jun 2020 20:28:07: 9000000 INFO @ Sun, 21 Jun 2020 20:28:08: 20000000 INFO @ Sun, 21 Jun 2020 20:28:12: 15000000 INFO @ Sun, 21 Jun 2020 20:28:13: 10000000 INFO @ Sun, 21 Jun 2020 20:28:14: 21000000 INFO @ Sun, 21 Jun 2020 20:28:17: 16000000 INFO @ Sun, 21 Jun 2020 20:28:18: 11000000 INFO @ Sun, 21 Jun 2020 20:28:19: 22000000 INFO @ Sun, 21 Jun 2020 20:28:23: 17000000 INFO @ Sun, 21 Jun 2020 20:28:24: 12000000 INFO @ Sun, 21 Jun 2020 20:28:25: 23000000 INFO @ Sun, 21 Jun 2020 20:28:29: 18000000 INFO @ Sun, 21 Jun 2020 20:28:30: 13000000 INFO @ Sun, 21 Jun 2020 20:28:31: 24000000 INFO @ Sun, 21 Jun 2020 20:28:34: 19000000 INFO @ Sun, 21 Jun 2020 20:28:35: 14000000 INFO @ Sun, 21 Jun 2020 20:28:36: 25000000 INFO @ Sun, 21 Jun 2020 20:28:40: 20000000 INFO @ Sun, 21 Jun 2020 20:28:41: 15000000 INFO @ Sun, 21 Jun 2020 20:28:42: 26000000 INFO @ Sun, 21 Jun 2020 20:28:45: 21000000 INFO @ Sun, 21 Jun 2020 20:28:46: 16000000 INFO @ Sun, 21 Jun 2020 20:28:48: 27000000 INFO @ Sun, 21 Jun 2020 20:28:50: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:28:50: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:28:50: #1 total tags in treatment: 27290790 INFO @ Sun, 21 Jun 2020 20:28:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:28:50: #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 20:28:50: #1 tags after filtering in treatment: 27290714 INFO @ Sun, 21 Jun 2020 20:28:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:28:50: #1 finished! INFO @ Sun, 21 Jun 2020 20:28:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:28:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:28:51: 22000000 INFO @ Sun, 21 Jun 2020 20:28:52: 17000000 INFO @ Sun, 21 Jun 2020 20:28:52: #2 number of paired peaks: 250 WARNING @ Sun, 21 Jun 2020 20:28:52: Fewer paired peaks (250) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 250 pairs to build model! INFO @ Sun, 21 Jun 2020 20:28:52: start model_add_line... INFO @ Sun, 21 Jun 2020 20:28:52: start X-correlation... INFO @ Sun, 21 Jun 2020 20:28:52: end of X-cor INFO @ Sun, 21 Jun 2020 20:28:52: #2 finished! INFO @ Sun, 21 Jun 2020 20:28:52: #2 predicted fragment length is 52 bps INFO @ Sun, 21 Jun 2020 20:28:52: #2 alternative fragment length(s) may be 1,52,533 bps INFO @ Sun, 21 Jun 2020 20:28:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981698/SRX3981698.05_model.r WARNING @ Sun, 21 Jun 2020 20:28:52: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:28:52: #2 You may need to consider one of the other alternative d(s): 1,52,533 WARNING @ Sun, 21 Jun 2020 20:28:52: #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 20:28:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:28:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:28:57: 23000000 INFO @ Sun, 21 Jun 2020 20:28:58: 18000000 INFO @ Sun, 21 Jun 2020 20:29:03: 24000000 INFO @ Sun, 21 Jun 2020 20:29:03: 19000000 INFO @ Sun, 21 Jun 2020 20:29:08: 25000000 INFO @ Sun, 21 Jun 2020 20:29:09: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:29:14: 26000000 INFO @ Sun, 21 Jun 2020 20:29:14: 21000000 INFO @ Sun, 21 Jun 2020 20:29:19: 27000000 INFO @ Sun, 21 Jun 2020 20:29:20: 22000000 INFO @ Sun, 21 Jun 2020 20:29:21: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:29:21: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:29:21: #1 total tags in treatment: 27290790 INFO @ Sun, 21 Jun 2020 20:29:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:29:21: #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 20:29:22: #1 tags after filtering in treatment: 27290714 INFO @ Sun, 21 Jun 2020 20:29:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:29:22: #1 finished! INFO @ Sun, 21 Jun 2020 20:29:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:29:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:29:24: #2 number of paired peaks: 250 WARNING @ Sun, 21 Jun 2020 20:29:24: Fewer paired peaks (250) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 250 pairs to build model! INFO @ Sun, 21 Jun 2020 20:29:24: start model_add_line... INFO @ Sun, 21 Jun 2020 20:29:24: start X-correlation... INFO @ Sun, 21 Jun 2020 20:29:24: end of X-cor INFO @ Sun, 21 Jun 2020 20:29:24: #2 finished! INFO @ Sun, 21 Jun 2020 20:29:24: #2 predicted fragment length is 52 bps INFO @ Sun, 21 Jun 2020 20:29:24: #2 alternative fragment length(s) may be 1,52,533 bps INFO @ Sun, 21 Jun 2020 20:29:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981698/SRX3981698.10_model.r WARNING @ Sun, 21 Jun 2020 20:29:24: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:29:24: #2 You may need to consider one of the other alternative d(s): 1,52,533 WARNING @ Sun, 21 Jun 2020 20:29:24: #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 20:29:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:29:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:29:25: 23000000 INFO @ Sun, 21 Jun 2020 20:29:31: 24000000 INFO @ Sun, 21 Jun 2020 20:29:36: 25000000 INFO @ Sun, 21 Jun 2020 20:29:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:29:42: 26000000 INFO @ Sun, 21 Jun 2020 20:29:47: 27000000 INFO @ Sun, 21 Jun 2020 20:29:49: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:29:49: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:29:49: #1 total tags in treatment: 27290790 INFO @ Sun, 21 Jun 2020 20:29:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:29:49: #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 20:29:49: #1 tags after filtering in treatment: 27290714 INFO @ Sun, 21 Jun 2020 20:29:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:29:49: #1 finished! INFO @ Sun, 21 Jun 2020 20:29:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:29:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:29:51: #2 number of paired peaks: 250 WARNING @ Sun, 21 Jun 2020 20:29:51: Fewer paired peaks (250) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 250 pairs to build model! INFO @ Sun, 21 Jun 2020 20:29:51: start model_add_line... INFO @ Sun, 21 Jun 2020 20:29:51: start X-correlation... INFO @ Sun, 21 Jun 2020 20:29:51: end of X-cor INFO @ Sun, 21 Jun 2020 20:29:51: #2 finished! INFO @ Sun, 21 Jun 2020 20:29:51: #2 predicted fragment length is 52 bps INFO @ Sun, 21 Jun 2020 20:29:51: #2 alternative fragment length(s) may be 1,52,533 bps INFO @ Sun, 21 Jun 2020 20:29:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981698/SRX3981698.20_model.r WARNING @ Sun, 21 Jun 2020 20:29:51: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:29:51: #2 You may need to consider one of the other alternative d(s): 1,52,533 WARNING @ Sun, 21 Jun 2020 20:29:51: #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 20:29:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:29:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:30:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981698/SRX3981698.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:30:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981698/SRX3981698.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:30:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981698/SRX3981698.05_summits.bed INFO @ Sun, 21 Jun 2020 20:30:05: Done! pass1 - making usageList (600 chroms): 2 millis pass2 - checking and writing primary data (3101 records, 4 fields): 18 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:30:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:30:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981698/SRX3981698.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:30:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981698/SRX3981698.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:30:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981698/SRX3981698.10_summits.bed INFO @ Sun, 21 Jun 2020 20:30:35: Done! pass1 - making usageList (364 chroms): 1 millis pass2 - checking and writing primary data (1241 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:30:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:31:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981698/SRX3981698.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:31:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981698/SRX3981698.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:31:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981698/SRX3981698.20_summits.bed INFO @ Sun, 21 Jun 2020 20:31:03: Done! pass1 - making usageList (148 chroms): 1 millis pass2 - checking and writing primary data (401 records, 4 fields): 6 millis CompletedMACS2peakCalling