Job ID = 6452777 SRX = SRX032118 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:59:08 prefetch.2.10.7: 1) Downloading 'SRR073939'... 2020-06-21T07:59:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:01:36 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:01:37 prefetch.2.10.7: 'SRR073939' is valid 2020-06-21T08:01:37 prefetch.2.10.7: 1) 'SRR073939' was downloaded successfully Read 25370460 spots for SRR073939/SRR073939.sra Written 25370460 spots for SRR073939/SRR073939.sra 2020-06-21T08:03:11 prefetch.2.10.7: 1) Downloading 'SRR073940'... 2020-06-21T08:03:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:07:57 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:07:58 prefetch.2.10.7: 'SRR073940' is valid 2020-06-21T08:07:58 prefetch.2.10.7: 1) 'SRR073940' was downloaded successfully Read 23050040 spots for SRR073940/SRR073940.sra Written 23050040 spots for SRR073940/SRR073940.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: 00:10:35 48420500 reads; of these: 48420500 (100.00%) were unpaired; of these: 941303 (1.94%) aligned 0 times 37799847 (78.07%) aligned exactly 1 time 9679350 (19.99%) aligned >1 times 98.06% overall alignment rate Time searching: 00:10:35 Overall time: 00:10:35 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] 17089691 / 47479197 = 0.3599 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 17:30:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX032118/SRX032118.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX032118/SRX032118.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX032118/SRX032118.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX032118/SRX032118.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 17:30:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:30:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:30:44: 1000000 INFO @ Sun, 21 Jun 2020 17:30:49: 2000000 INFO @ Sun, 21 Jun 2020 17:30:54: 3000000 INFO @ Sun, 21 Jun 2020 17:30:58: 4000000 INFO @ Sun, 21 Jun 2020 17:31:03: 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 17:31:08: 6000000 INFO @ Sun, 21 Jun 2020 17:31:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX032118/SRX032118.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX032118/SRX032118.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX032118/SRX032118.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX032118/SRX032118.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 17:31:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:31:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:31:13: 7000000 INFO @ Sun, 21 Jun 2020 17:31:14: 1000000 INFO @ Sun, 21 Jun 2020 17:31:18: 8000000 INFO @ Sun, 21 Jun 2020 17:31:19: 2000000 INFO @ Sun, 21 Jun 2020 17:31:23: 9000000 INFO @ Sun, 21 Jun 2020 17:31:24: 3000000 INFO @ Sun, 21 Jun 2020 17:31:28: 10000000 INFO @ Sun, 21 Jun 2020 17:31:29: 4000000 INFO @ Sun, 21 Jun 2020 17:31:34: 11000000 INFO @ Sun, 21 Jun 2020 17:31:35: 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 17:31:39: 12000000 INFO @ Sun, 21 Jun 2020 17:31:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX032118/SRX032118.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX032118/SRX032118.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX032118/SRX032118.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX032118/SRX032118.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 17:31:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:31:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:31:40: 6000000 INFO @ Sun, 21 Jun 2020 17:31:45: 13000000 INFO @ Sun, 21 Jun 2020 17:31:45: 1000000 INFO @ Sun, 21 Jun 2020 17:31:46: 7000000 INFO @ Sun, 21 Jun 2020 17:31:50: 14000000 INFO @ Sun, 21 Jun 2020 17:31:51: 2000000 INFO @ Sun, 21 Jun 2020 17:31:51: 8000000 INFO @ Sun, 21 Jun 2020 17:31:56: 15000000 INFO @ Sun, 21 Jun 2020 17:31:56: 3000000 INFO @ Sun, 21 Jun 2020 17:31:57: 9000000 INFO @ Sun, 21 Jun 2020 17:32:01: 16000000 INFO @ Sun, 21 Jun 2020 17:32:02: 10000000 INFO @ Sun, 21 Jun 2020 17:32:02: 4000000 INFO @ Sun, 21 Jun 2020 17:32:07: 17000000 INFO @ Sun, 21 Jun 2020 17:32:08: 11000000 INFO @ Sun, 21 Jun 2020 17:32:08: 5000000 INFO @ Sun, 21 Jun 2020 17:32:12: 18000000 INFO @ Sun, 21 Jun 2020 17:32:13: 12000000 INFO @ Sun, 21 Jun 2020 17:32:13: 6000000 INFO @ Sun, 21 Jun 2020 17:32:18: 19000000 INFO @ Sun, 21 Jun 2020 17:32:19: 13000000 INFO @ Sun, 21 Jun 2020 17:32:19: 7000000 INFO @ Sun, 21 Jun 2020 17:32:23: 20000000 INFO @ Sun, 21 Jun 2020 17:32:24: 14000000 INFO @ Sun, 21 Jun 2020 17:32:24: 8000000 INFO @ Sun, 21 Jun 2020 17:32:29: 21000000 INFO @ Sun, 21 Jun 2020 17:32:29: 15000000 INFO @ Sun, 21 Jun 2020 17:32:30: 9000000 INFO @ Sun, 21 Jun 2020 17:32:34: 22000000 INFO @ Sun, 21 Jun 2020 17:32:35: 16000000 INFO @ Sun, 21 Jun 2020 17:32:35: 10000000 INFO @ Sun, 21 Jun 2020 17:32:40: 23000000 INFO @ Sun, 21 Jun 2020 17:32:40: 17000000 INFO @ Sun, 21 Jun 2020 17:32:41: 11000000 INFO @ Sun, 21 Jun 2020 17:32:45: 24000000 INFO @ Sun, 21 Jun 2020 17:32:46: 18000000 INFO @ Sun, 21 Jun 2020 17:32:46: 12000000 INFO @ Sun, 21 Jun 2020 17:32:51: 19000000 INFO @ Sun, 21 Jun 2020 17:32:52: 13000000 INFO @ Sun, 21 Jun 2020 17:32:52: 25000000 INFO @ Sun, 21 Jun 2020 17:32:57: 20000000 INFO @ Sun, 21 Jun 2020 17:32:57: 14000000 INFO @ Sun, 21 Jun 2020 17:32:57: 26000000 INFO @ Sun, 21 Jun 2020 17:33:02: 21000000 INFO @ Sun, 21 Jun 2020 17:33:03: 15000000 INFO @ Sun, 21 Jun 2020 17:33:03: 27000000 INFO @ Sun, 21 Jun 2020 17:33:07: 22000000 INFO @ Sun, 21 Jun 2020 17:33:08: 16000000 INFO @ Sun, 21 Jun 2020 17:33:09: 28000000 INFO @ Sun, 21 Jun 2020 17:33:13: 23000000 INFO @ Sun, 21 Jun 2020 17:33:13: 17000000 INFO @ Sun, 21 Jun 2020 17:33:15: 29000000 INFO @ Sun, 21 Jun 2020 17:33:18: 24000000 INFO @ Sun, 21 Jun 2020 17:33:19: 18000000 INFO @ Sun, 21 Jun 2020 17:33:22: 30000000 INFO @ Sun, 21 Jun 2020 17:33:24: 19000000 INFO @ Sun, 21 Jun 2020 17:33:24: 25000000 INFO @ Sun, 21 Jun 2020 17:33:25: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:33:25: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:33:25: #1 total tags in treatment: 30389506 INFO @ Sun, 21 Jun 2020 17:33:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:33:25: #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 17:33:27: #1 tags after filtering in treatment: 30389493 INFO @ Sun, 21 Jun 2020 17:33:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:33:27: #1 finished! INFO @ Sun, 21 Jun 2020 17:33:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:33:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:33:28: 20000000 INFO @ Sun, 21 Jun 2020 17:33:29: 26000000 INFO @ Sun, 21 Jun 2020 17:33:29: #2 number of paired peaks: 363 WARNING @ Sun, 21 Jun 2020 17:33:29: Fewer paired peaks (363) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 363 pairs to build model! INFO @ Sun, 21 Jun 2020 17:33:29: start model_add_line... INFO @ Sun, 21 Jun 2020 17:33:29: start X-correlation... INFO @ Sun, 21 Jun 2020 17:33:29: end of X-cor INFO @ Sun, 21 Jun 2020 17:33:29: #2 finished! INFO @ Sun, 21 Jun 2020 17:33:29: #2 predicted fragment length is 304 bps INFO @ Sun, 21 Jun 2020 17:33:29: #2 alternative fragment length(s) may be 304 bps INFO @ Sun, 21 Jun 2020 17:33:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX032118/SRX032118.05_model.r INFO @ Sun, 21 Jun 2020 17:33:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:33:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:33:33: 21000000 INFO @ Sun, 21 Jun 2020 17:33:34: 27000000 INFO @ Sun, 21 Jun 2020 17:33:39: 22000000 INFO @ Sun, 21 Jun 2020 17:33:39: 28000000 INFO @ Sun, 21 Jun 2020 17:33:44: 23000000 INFO @ Sun, 21 Jun 2020 17:33:44: 29000000 INFO @ Sun, 21 Jun 2020 17:33:49: 24000000 INFO @ Sun, 21 Jun 2020 17:33:50: 30000000 INFO @ Sun, 21 Jun 2020 17:33:53: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:33:53: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:33:53: #1 total tags in treatment: 30389506 INFO @ Sun, 21 Jun 2020 17:33:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:33:53: #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 17:33:54: #1 tags after filtering in treatment: 30389493 INFO @ Sun, 21 Jun 2020 17:33:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:33:54: #1 finished! INFO @ Sun, 21 Jun 2020 17:33:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:33:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:33:55: 25000000 INFO @ Sun, 21 Jun 2020 17:33:56: #2 number of paired peaks: 363 WARNING @ Sun, 21 Jun 2020 17:33:56: Fewer paired peaks (363) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 363 pairs to build model! INFO @ Sun, 21 Jun 2020 17:33:56: start model_add_line... INFO @ Sun, 21 Jun 2020 17:33:56: start X-correlation... INFO @ Sun, 21 Jun 2020 17:33:56: end of X-cor INFO @ Sun, 21 Jun 2020 17:33:56: #2 finished! INFO @ Sun, 21 Jun 2020 17:33:56: #2 predicted fragment length is 304 bps INFO @ Sun, 21 Jun 2020 17:33:56: #2 alternative fragment length(s) may be 304 bps INFO @ Sun, 21 Jun 2020 17:33:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX032118/SRX032118.10_model.r INFO @ Sun, 21 Jun 2020 17:33:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:33:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:34:00: 26000000 INFO @ Sun, 21 Jun 2020 17:34:04: 27000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:34:09: 28000000 INFO @ Sun, 21 Jun 2020 17:34:14: 29000000 INFO @ Sun, 21 Jun 2020 17:34:19: 30000000 INFO @ Sun, 21 Jun 2020 17:34:21: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:34:21: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:34:21: #1 total tags in treatment: 30389506 INFO @ Sun, 21 Jun 2020 17:34:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:34:21: #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 17:34:22: #1 tags after filtering in treatment: 30389493 INFO @ Sun, 21 Jun 2020 17:34:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:34:22: #1 finished! INFO @ Sun, 21 Jun 2020 17:34:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:34:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:34:24: #2 number of paired peaks: 363 WARNING @ Sun, 21 Jun 2020 17:34:24: Fewer paired peaks (363) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 363 pairs to build model! INFO @ Sun, 21 Jun 2020 17:34:24: start model_add_line... INFO @ Sun, 21 Jun 2020 17:34:24: start X-correlation... INFO @ Sun, 21 Jun 2020 17:34:24: end of X-cor INFO @ Sun, 21 Jun 2020 17:34:24: #2 finished! INFO @ Sun, 21 Jun 2020 17:34:24: #2 predicted fragment length is 304 bps INFO @ Sun, 21 Jun 2020 17:34:24: #2 alternative fragment length(s) may be 304 bps INFO @ Sun, 21 Jun 2020 17:34:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX032118/SRX032118.20_model.r INFO @ Sun, 21 Jun 2020 17:34:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:34:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:34:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:34:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:34:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX032118/SRX032118.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:34:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX032118/SRX032118.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:34:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX032118/SRX032118.05_summits.bed INFO @ Sun, 21 Jun 2020 17:34:59: Done! pass1 - making usageList (511 chroms): 1 millis pass2 - checking and writing primary data (2243 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:35:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX032118/SRX032118.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:35:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX032118/SRX032118.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:35:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX032118/SRX032118.10_summits.bed INFO @ Sun, 21 Jun 2020 17:35:24: Done! pass1 - making usageList (460 chroms): 2 millis pass2 - checking and writing primary data (1424 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:35:27: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:35:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX032118/SRX032118.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:35:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX032118/SRX032118.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:35:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX032118/SRX032118.20_summits.bed INFO @ Sun, 21 Jun 2020 17:35:53: Done! pass1 - making usageList (407 chroms): 1 millis pass2 - checking and writing primary data (955 records, 4 fields): 48 millis CompletedMACS2peakCalling