Job ID = 6498308 SRX = SRX467119 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T23:55:14 prefetch.2.10.7: 1) Downloading 'SRR1164543'... 2020-06-25T23:55:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:57:53 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:57:53 prefetch.2.10.7: 1) 'SRR1164543' was downloaded successfully Read 23815812 spots for SRR1164543/SRR1164543.sra Written 23815812 spots for SRR1164543/SRR1164543.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: 00:10:16 23815812 reads; of these: 23815812 (100.00%) were unpaired; of these: 1202671 (5.05%) aligned 0 times 14617373 (61.38%) aligned exactly 1 time 7995768 (33.57%) aligned >1 times 94.95% overall alignment rate Time searching: 00:10:16 Overall time: 00:10:16 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 3939526 / 22613141 = 0.1742 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 @ Fri, 26 Jun 2020 09:16:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467119/SRX467119.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467119/SRX467119.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467119/SRX467119.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467119/SRX467119.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 @ Fri, 26 Jun 2020 09:16:41: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:16:41: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:16:48: 1000000 INFO @ Fri, 26 Jun 2020 09:16:55: 2000000 INFO @ Fri, 26 Jun 2020 09:17:03: 3000000 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 @ Fri, 26 Jun 2020 09:17:10: 4000000 INFO @ Fri, 26 Jun 2020 09:17:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467119/SRX467119.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467119/SRX467119.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467119/SRX467119.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467119/SRX467119.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 @ Fri, 26 Jun 2020 09:17:11: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:17:11: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:17:17: 5000000 INFO @ Fri, 26 Jun 2020 09:17:18: 1000000 INFO @ Fri, 26 Jun 2020 09:17:24: 6000000 INFO @ Fri, 26 Jun 2020 09:17:25: 2000000 INFO @ Fri, 26 Jun 2020 09:17:32: 7000000 INFO @ Fri, 26 Jun 2020 09:17:32: 3000000 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 @ Fri, 26 Jun 2020 09:17:39: 8000000 INFO @ Fri, 26 Jun 2020 09:17:39: 4000000 INFO @ Fri, 26 Jun 2020 09:17:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467119/SRX467119.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467119/SRX467119.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467119/SRX467119.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467119/SRX467119.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 @ Fri, 26 Jun 2020 09:17:41: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:17:41: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:17:46: 9000000 INFO @ Fri, 26 Jun 2020 09:17:47: 5000000 INFO @ Fri, 26 Jun 2020 09:17:48: 1000000 INFO @ Fri, 26 Jun 2020 09:17:54: 10000000 INFO @ Fri, 26 Jun 2020 09:17:54: 6000000 INFO @ Fri, 26 Jun 2020 09:17:55: 2000000 INFO @ Fri, 26 Jun 2020 09:18:01: 11000000 INFO @ Fri, 26 Jun 2020 09:18:02: 7000000 INFO @ Fri, 26 Jun 2020 09:18:03: 3000000 INFO @ Fri, 26 Jun 2020 09:18:08: 12000000 INFO @ Fri, 26 Jun 2020 09:18:09: 8000000 INFO @ Fri, 26 Jun 2020 09:18:10: 4000000 INFO @ Fri, 26 Jun 2020 09:18:15: 13000000 INFO @ Fri, 26 Jun 2020 09:18:16: 9000000 INFO @ Fri, 26 Jun 2020 09:18:18: 5000000 INFO @ Fri, 26 Jun 2020 09:18:22: 14000000 INFO @ Fri, 26 Jun 2020 09:18:23: 10000000 INFO @ Fri, 26 Jun 2020 09:18:25: 6000000 INFO @ Fri, 26 Jun 2020 09:18:29: 15000000 INFO @ Fri, 26 Jun 2020 09:18:30: 11000000 INFO @ Fri, 26 Jun 2020 09:18:32: 7000000 INFO @ Fri, 26 Jun 2020 09:18:36: 16000000 INFO @ Fri, 26 Jun 2020 09:18:37: 12000000 INFO @ Fri, 26 Jun 2020 09:18:40: 8000000 INFO @ Fri, 26 Jun 2020 09:18:43: 17000000 INFO @ Fri, 26 Jun 2020 09:18:44: 13000000 INFO @ Fri, 26 Jun 2020 09:18:47: 9000000 INFO @ Fri, 26 Jun 2020 09:18:50: 18000000 INFO @ Fri, 26 Jun 2020 09:18:51: 14000000 INFO @ Fri, 26 Jun 2020 09:18:54: 10000000 INFO @ Fri, 26 Jun 2020 09:18:55: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:18:55: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:18:55: #1 total tags in treatment: 18673615 INFO @ Fri, 26 Jun 2020 09:18:55: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:18:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:18:56: #1 tags after filtering in treatment: 18673615 INFO @ Fri, 26 Jun 2020 09:18:56: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:18:56: #1 finished! INFO @ Fri, 26 Jun 2020 09:18:56: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:18:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:18:57: #2 number of paired peaks: 233 WARNING @ Fri, 26 Jun 2020 09:18:57: Fewer paired peaks (233) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 233 pairs to build model! INFO @ Fri, 26 Jun 2020 09:18:57: start model_add_line... INFO @ Fri, 26 Jun 2020 09:18:57: start X-correlation... INFO @ Fri, 26 Jun 2020 09:18:57: end of X-cor INFO @ Fri, 26 Jun 2020 09:18:57: #2 finished! INFO @ Fri, 26 Jun 2020 09:18:57: #2 predicted fragment length is 41 bps INFO @ Fri, 26 Jun 2020 09:18:57: #2 alternative fragment length(s) may be 41 bps INFO @ Fri, 26 Jun 2020 09:18:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX467119/SRX467119.05_model.r WARNING @ Fri, 26 Jun 2020 09:18:57: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:18:57: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Fri, 26 Jun 2020 09:18:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 09:18:57: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:18:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:18:57: 15000000 INFO @ Fri, 26 Jun 2020 09:19:00: 11000000 INFO @ Fri, 26 Jun 2020 09:19:03: 16000000 INFO @ Fri, 26 Jun 2020 09:19:06: 12000000 INFO @ Fri, 26 Jun 2020 09:19:10: 17000000 INFO @ Fri, 26 Jun 2020 09:19:12: 13000000 INFO @ Fri, 26 Jun 2020 09:19:17: 18000000 INFO @ Fri, 26 Jun 2020 09:19:18: 14000000 INFO @ Fri, 26 Jun 2020 09:19:21: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:19:21: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:19:21: #1 total tags in treatment: 18673615 INFO @ Fri, 26 Jun 2020 09:19:21: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:19:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:19:22: #1 tags after filtering in treatment: 18673615 INFO @ Fri, 26 Jun 2020 09:19:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:19:22: #1 finished! INFO @ Fri, 26 Jun 2020 09:19:22: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:19:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:19:23: #2 number of paired peaks: 233 WARNING @ Fri, 26 Jun 2020 09:19:23: Fewer paired peaks (233) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 233 pairs to build model! INFO @ Fri, 26 Jun 2020 09:19:23: start model_add_line... INFO @ Fri, 26 Jun 2020 09:19:23: start X-correlation... INFO @ Fri, 26 Jun 2020 09:19:23: end of X-cor INFO @ Fri, 26 Jun 2020 09:19:23: #2 finished! INFO @ Fri, 26 Jun 2020 09:19:23: #2 predicted fragment length is 41 bps INFO @ Fri, 26 Jun 2020 09:19:23: #2 alternative fragment length(s) may be 41 bps INFO @ Fri, 26 Jun 2020 09:19:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX467119/SRX467119.10_model.r WARNING @ Fri, 26 Jun 2020 09:19:23: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:19:23: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Fri, 26 Jun 2020 09:19:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 09:19:23: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:19:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:19:24: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:19:29: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:19:29: 16000000 INFO @ Fri, 26 Jun 2020 09:19:35: 17000000 INFO @ Fri, 26 Jun 2020 09:19:41: 18000000 INFO @ Fri, 26 Jun 2020 09:19:45: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:19:45: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:19:45: #1 total tags in treatment: 18673615 INFO @ Fri, 26 Jun 2020 09:19:45: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:19:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:19:45: #1 tags after filtering in treatment: 18673615 INFO @ Fri, 26 Jun 2020 09:19:45: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:19:45: #1 finished! INFO @ Fri, 26 Jun 2020 09:19:45: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:19:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:19:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX467119/SRX467119.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:19:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX467119/SRX467119.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:19:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX467119/SRX467119.05_summits.bed INFO @ Fri, 26 Jun 2020 09:19:46: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2745 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:19:46: #2 number of paired peaks: 233 WARNING @ Fri, 26 Jun 2020 09:19:46: Fewer paired peaks (233) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 233 pairs to build model! INFO @ Fri, 26 Jun 2020 09:19:46: start model_add_line... INFO @ Fri, 26 Jun 2020 09:19:46: start X-correlation... INFO @ Fri, 26 Jun 2020 09:19:46: end of X-cor INFO @ Fri, 26 Jun 2020 09:19:46: #2 finished! INFO @ Fri, 26 Jun 2020 09:19:46: #2 predicted fragment length is 41 bps INFO @ Fri, 26 Jun 2020 09:19:46: #2 alternative fragment length(s) may be 41 bps INFO @ Fri, 26 Jun 2020 09:19:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX467119/SRX467119.20_model.r WARNING @ Fri, 26 Jun 2020 09:19:46: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:19:46: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Fri, 26 Jun 2020 09:19:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 09:19:46: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:19:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:19:54: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:20:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX467119/SRX467119.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:20:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX467119/SRX467119.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:20:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX467119/SRX467119.10_summits.bed INFO @ Fri, 26 Jun 2020 09:20:11: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2044 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:20:17: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 09:20:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX467119/SRX467119.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:20:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX467119/SRX467119.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:20:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX467119/SRX467119.20_summits.bed INFO @ Fri, 26 Jun 2020 09:20:34: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1445 records, 4 fields): 4 millis CompletedMACS2peakCalling