Job ID = 6456276 SRX = SRX331425 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:37:14 prefetch.2.10.7: 1) Downloading 'SRR947662'... 2020-06-21T10:37:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:40:00 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:40:00 prefetch.2.10.7: 1) 'SRR947662' was downloaded successfully Read 18127616 spots for SRR947662/SRR947662.sra Written 18127616 spots for SRR947662/SRR947662.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: 00:05:41 18127616 reads; of these: 18127616 (100.00%) were unpaired; of these: 1064724 (5.87%) aligned 0 times 10988577 (60.62%) aligned exactly 1 time 6074315 (33.51%) aligned >1 times 94.13% overall alignment rate Time searching: 00:05:41 Overall time: 00:05:41 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] 3492862 / 17062892 = 0.2047 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 19:51:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331425/SRX331425.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331425/SRX331425.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331425/SRX331425.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331425/SRX331425.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 19:51:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:51:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:51:36: 1000000 INFO @ Sun, 21 Jun 2020 19:51:42: 2000000 INFO @ Sun, 21 Jun 2020 19:51:49: 3000000 INFO @ Sun, 21 Jun 2020 19:51:55: 4000000 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 19:52:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331425/SRX331425.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331425/SRX331425.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331425/SRX331425.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331425/SRX331425.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 19:52:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:52:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:52:01: 5000000 INFO @ Sun, 21 Jun 2020 19:52:07: 1000000 INFO @ Sun, 21 Jun 2020 19:52:07: 6000000 INFO @ Sun, 21 Jun 2020 19:52:13: 2000000 INFO @ Sun, 21 Jun 2020 19:52:14: 7000000 INFO @ Sun, 21 Jun 2020 19:52:20: 3000000 INFO @ Sun, 21 Jun 2020 19:52:20: 8000000 INFO @ Sun, 21 Jun 2020 19:52:26: 4000000 INFO @ Sun, 21 Jun 2020 19:52:27: 9000000 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 19:52:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331425/SRX331425.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331425/SRX331425.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331425/SRX331425.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331425/SRX331425.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 19:52:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:52:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:52:33: 5000000 INFO @ Sun, 21 Jun 2020 19:52:33: 10000000 INFO @ Sun, 21 Jun 2020 19:52:36: 1000000 INFO @ Sun, 21 Jun 2020 19:52:39: 6000000 INFO @ Sun, 21 Jun 2020 19:52:40: 11000000 INFO @ Sun, 21 Jun 2020 19:52:43: 2000000 INFO @ Sun, 21 Jun 2020 19:52:45: 7000000 INFO @ Sun, 21 Jun 2020 19:52:47: 12000000 INFO @ Sun, 21 Jun 2020 19:52:49: 3000000 INFO @ Sun, 21 Jun 2020 19:52:52: 8000000 INFO @ Sun, 21 Jun 2020 19:52:53: 13000000 INFO @ Sun, 21 Jun 2020 19:52:56: 4000000 INFO @ Sun, 21 Jun 2020 19:52:57: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:52:57: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:52:57: #1 total tags in treatment: 13570030 INFO @ Sun, 21 Jun 2020 19:52:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:52:57: #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 19:52:58: #1 tags after filtering in treatment: 13570030 INFO @ Sun, 21 Jun 2020 19:52:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:52:58: #1 finished! INFO @ Sun, 21 Jun 2020 19:52:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:52:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:52:58: 9000000 INFO @ Sun, 21 Jun 2020 19:52:59: #2 number of paired peaks: 1134 INFO @ Sun, 21 Jun 2020 19:52:59: start model_add_line... INFO @ Sun, 21 Jun 2020 19:52:59: start X-correlation... INFO @ Sun, 21 Jun 2020 19:52:59: end of X-cor INFO @ Sun, 21 Jun 2020 19:52:59: #2 finished! INFO @ Sun, 21 Jun 2020 19:52:59: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 19:52:59: #2 alternative fragment length(s) may be 3,47 bps INFO @ Sun, 21 Jun 2020 19:52:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331425/SRX331425.05_model.r WARNING @ Sun, 21 Jun 2020 19:52:59: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:52:59: #2 You may need to consider one of the other alternative d(s): 3,47 WARNING @ Sun, 21 Jun 2020 19:52:59: #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 19:52:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:52:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:53:02: 5000000 INFO @ Sun, 21 Jun 2020 19:53:05: 10000000 INFO @ Sun, 21 Jun 2020 19:53:09: 6000000 INFO @ Sun, 21 Jun 2020 19:53:11: 11000000 INFO @ Sun, 21 Jun 2020 19:53:15: 7000000 INFO @ Sun, 21 Jun 2020 19:53:18: 12000000 INFO @ Sun, 21 Jun 2020 19:53:22: 8000000 INFO @ Sun, 21 Jun 2020 19:53:24: 13000000 INFO @ Sun, 21 Jun 2020 19:53:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:53:28: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:53:28: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:53:28: #1 total tags in treatment: 13570030 INFO @ Sun, 21 Jun 2020 19:53:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:53:28: #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 19:53:28: 9000000 INFO @ Sun, 21 Jun 2020 19:53:29: #1 tags after filtering in treatment: 13570030 INFO @ Sun, 21 Jun 2020 19:53:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:53:29: #1 finished! INFO @ Sun, 21 Jun 2020 19:53:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:53:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:53:30: #2 number of paired peaks: 1134 INFO @ Sun, 21 Jun 2020 19:53:30: start model_add_line... INFO @ Sun, 21 Jun 2020 19:53:30: start X-correlation... INFO @ Sun, 21 Jun 2020 19:53:30: end of X-cor INFO @ Sun, 21 Jun 2020 19:53:30: #2 finished! INFO @ Sun, 21 Jun 2020 19:53:30: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 19:53:30: #2 alternative fragment length(s) may be 3,47 bps INFO @ Sun, 21 Jun 2020 19:53:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331425/SRX331425.10_model.r WARNING @ Sun, 21 Jun 2020 19:53:30: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:53:30: #2 You may need to consider one of the other alternative d(s): 3,47 WARNING @ Sun, 21 Jun 2020 19:53:30: #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 19:53:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:53:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:53:35: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:53:41: 11000000 INFO @ Sun, 21 Jun 2020 19:53:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331425/SRX331425.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:53:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331425/SRX331425.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:53:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331425/SRX331425.05_summits.bed INFO @ Sun, 21 Jun 2020 19:53:42: Done! pass1 - making usageList (651 chroms): 2 millis pass2 - checking and writing primary data (2949 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:53:48: 12000000 INFO @ Sun, 21 Jun 2020 19:53:55: 13000000 INFO @ Sun, 21 Jun 2020 19:53:59: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:53:59: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:53:59: #1 total tags in treatment: 13570030 INFO @ Sun, 21 Jun 2020 19:53:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:53:59: #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 19:53:59: #1 tags after filtering in treatment: 13570030 INFO @ Sun, 21 Jun 2020 19:53:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:53:59: #1 finished! INFO @ Sun, 21 Jun 2020 19:53:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:53:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:54:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:54:01: #2 number of paired peaks: 1134 INFO @ Sun, 21 Jun 2020 19:54:01: start model_add_line... INFO @ Sun, 21 Jun 2020 19:54:01: start X-correlation... INFO @ Sun, 21 Jun 2020 19:54:01: end of X-cor INFO @ Sun, 21 Jun 2020 19:54:01: #2 finished! INFO @ Sun, 21 Jun 2020 19:54:01: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 19:54:01: #2 alternative fragment length(s) may be 3,47 bps INFO @ Sun, 21 Jun 2020 19:54:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331425/SRX331425.20_model.r WARNING @ Sun, 21 Jun 2020 19:54:01: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:54:01: #2 You may need to consider one of the other alternative d(s): 3,47 WARNING @ Sun, 21 Jun 2020 19:54:01: #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 19:54:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:54:01: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:54:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331425/SRX331425.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:54:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331425/SRX331425.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:54:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331425/SRX331425.10_summits.bed INFO @ Sun, 21 Jun 2020 19:54:14: Done! pass1 - making usageList (567 chroms): 2 millis pass2 - checking and writing primary data (2278 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:54:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:54:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331425/SRX331425.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:54:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331425/SRX331425.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:54:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331425/SRX331425.20_summits.bed INFO @ Sun, 21 Jun 2020 19:54:45: Done! pass1 - making usageList (383 chroms): 2 millis pass2 - checking and writing primary data (943 records, 4 fields): 12 millis CompletedMACS2peakCalling