Job ID = 6458987 SRX = SRX5849998 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:58:05 prefetch.2.10.7: 1) Downloading 'SRR9074474'... 2020-06-21T12:58:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:02:51 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:02:51 prefetch.2.10.7: 1) 'SRR9074474' was downloaded successfully Read 40463033 spots for SRR9074474/SRR9074474.sra Written 40463033 spots for SRR9074474/SRR9074474.sra 2020-06-21T13:05:34 prefetch.2.10.7: 1) Downloading 'SRR9074475'... 2020-06-21T13:05:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:07:06 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:07:06 prefetch.2.10.7: 'SRR9074475' is valid 2020-06-21T13:07:06 prefetch.2.10.7: 1) 'SRR9074475' was downloaded successfully 2020-06-21T13:07:06 prefetch.2.10.7: 'SRR9074475' has 0 unresolved dependencies Read 15459531 spots for SRR9074475/SRR9074475.sra Written 15459531 spots for SRR9074475/SRR9074475.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: 00:06:53 55922564 reads; of these: 55922564 (100.00%) were unpaired; of these: 45962640 (82.19%) aligned 0 times 7208468 (12.89%) aligned exactly 1 time 2751456 (4.92%) aligned >1 times 17.81% overall alignment rate Time searching: 00:06:53 Overall time: 00:06:53 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 8 files... [bam_rmdupse_core] 1292497 / 9959924 = 0.1298 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 22:17:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5849998/SRX5849998.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5849998/SRX5849998.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5849998/SRX5849998.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5849998/SRX5849998.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 22:17:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:17:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:17:40: 1000000 INFO @ Sun, 21 Jun 2020 22:17:44: 2000000 INFO @ Sun, 21 Jun 2020 22:17:49: 3000000 INFO @ Sun, 21 Jun 2020 22:17:54: 4000000 INFO @ Sun, 21 Jun 2020 22:17:58: 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 22:18:03: 6000000 INFO @ Sun, 21 Jun 2020 22:18:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5849998/SRX5849998.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5849998/SRX5849998.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5849998/SRX5849998.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5849998/SRX5849998.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 22:18:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:18:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:18:08: 7000000 INFO @ Sun, 21 Jun 2020 22:18:11: 1000000 INFO @ Sun, 21 Jun 2020 22:18:13: 8000000 INFO @ Sun, 21 Jun 2020 22:18:17: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:18:17: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:18:17: #1 total tags in treatment: 8667427 INFO @ Sun, 21 Jun 2020 22:18:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:18:17: #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 22:18:17: 2000000 INFO @ Sun, 21 Jun 2020 22:18:17: #1 tags after filtering in treatment: 8667290 INFO @ Sun, 21 Jun 2020 22:18:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:18:17: #1 finished! INFO @ Sun, 21 Jun 2020 22:18:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:18:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:18:18: #2 number of paired peaks: 5962 INFO @ Sun, 21 Jun 2020 22:18:18: start model_add_line... INFO @ Sun, 21 Jun 2020 22:18:18: start X-correlation... INFO @ Sun, 21 Jun 2020 22:18:18: end of X-cor INFO @ Sun, 21 Jun 2020 22:18:18: #2 finished! INFO @ Sun, 21 Jun 2020 22:18:18: #2 predicted fragment length is 192 bps INFO @ Sun, 21 Jun 2020 22:18:18: #2 alternative fragment length(s) may be 2,192 bps INFO @ Sun, 21 Jun 2020 22:18:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5849998/SRX5849998.05_model.r INFO @ Sun, 21 Jun 2020 22:18:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:18:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:18:23: 3000000 INFO @ Sun, 21 Jun 2020 22:18:29: 4000000 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 22:18:34: 5000000 INFO @ Sun, 21 Jun 2020 22:18:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5849998/SRX5849998.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5849998/SRX5849998.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5849998/SRX5849998.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5849998/SRX5849998.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 22:18:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:18:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:18:40: 1000000 INFO @ Sun, 21 Jun 2020 22:18:40: 6000000 INFO @ Sun, 21 Jun 2020 22:18:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:18:45: 2000000 INFO @ Sun, 21 Jun 2020 22:18:46: 7000000 INFO @ Sun, 21 Jun 2020 22:18:50: 3000000 INFO @ Sun, 21 Jun 2020 22:18:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5849998/SRX5849998.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:18:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5849998/SRX5849998.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:18:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5849998/SRX5849998.05_summits.bed INFO @ Sun, 21 Jun 2020 22:18:52: Done! INFO @ Sun, 21 Jun 2020 22:18:52: 8000000 pass1 - making usageList (236 chroms): 1 millis pass2 - checking and writing primary data (6144 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:18:55: 4000000 INFO @ Sun, 21 Jun 2020 22:18:56: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:18:56: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:18:56: #1 total tags in treatment: 8667427 INFO @ Sun, 21 Jun 2020 22:18:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:18:56: #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 22:18:57: #1 tags after filtering in treatment: 8667290 INFO @ Sun, 21 Jun 2020 22:18:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:18:57: #1 finished! INFO @ Sun, 21 Jun 2020 22:18:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:18:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:18:58: #2 number of paired peaks: 5962 INFO @ Sun, 21 Jun 2020 22:18:58: start model_add_line... INFO @ Sun, 21 Jun 2020 22:18:58: start X-correlation... INFO @ Sun, 21 Jun 2020 22:18:58: end of X-cor INFO @ Sun, 21 Jun 2020 22:18:58: #2 finished! INFO @ Sun, 21 Jun 2020 22:18:58: #2 predicted fragment length is 192 bps INFO @ Sun, 21 Jun 2020 22:18:58: #2 alternative fragment length(s) may be 2,192 bps INFO @ Sun, 21 Jun 2020 22:18:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5849998/SRX5849998.10_model.r INFO @ Sun, 21 Jun 2020 22:18:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:18:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:19:00: 5000000 INFO @ Sun, 21 Jun 2020 22:19:05: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:19:10: 7000000 INFO @ Sun, 21 Jun 2020 22:19:15: 8000000 INFO @ Sun, 21 Jun 2020 22:19:18: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:19:18: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:19:18: #1 total tags in treatment: 8667427 INFO @ Sun, 21 Jun 2020 22:19:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:19:18: #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 22:19:19: #1 tags after filtering in treatment: 8667290 INFO @ Sun, 21 Jun 2020 22:19:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:19:19: #1 finished! INFO @ Sun, 21 Jun 2020 22:19:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:19:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:19:20: #2 number of paired peaks: 5962 INFO @ Sun, 21 Jun 2020 22:19:20: start model_add_line... INFO @ Sun, 21 Jun 2020 22:19:20: start X-correlation... INFO @ Sun, 21 Jun 2020 22:19:20: end of X-cor INFO @ Sun, 21 Jun 2020 22:19:20: #2 finished! INFO @ Sun, 21 Jun 2020 22:19:20: #2 predicted fragment length is 192 bps INFO @ Sun, 21 Jun 2020 22:19:20: #2 alternative fragment length(s) may be 2,192 bps INFO @ Sun, 21 Jun 2020 22:19:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5849998/SRX5849998.20_model.r INFO @ Sun, 21 Jun 2020 22:19:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:19:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:19:21: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:19:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5849998/SRX5849998.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:19:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5849998/SRX5849998.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:19:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5849998/SRX5849998.10_summits.bed INFO @ Sun, 21 Jun 2020 22:19:32: Done! pass1 - making usageList (199 chroms): 1 millis pass2 - checking and writing primary data (2484 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:19:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:19:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5849998/SRX5849998.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:19:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5849998/SRX5849998.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:19:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5849998/SRX5849998.20_summits.bed INFO @ Sun, 21 Jun 2020 22:19:51: Done! pass1 - making usageList (144 chroms): 1 millis pass2 - checking and writing primary data (668 records, 4 fields): 5 millis CompletedMACS2peakCalling