Job ID = 6528389 SRX = SRX5717025 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T14:50:25 prefetch.2.10.7: 1) Downloading 'SRR8936385'... 2020-06-29T14:50:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:51:58 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:51:58 prefetch.2.10.7: 1) 'SRR8936385' was downloaded successfully Read 27306349 spots for SRR8936385/SRR8936385.sra Written 27306349 spots for SRR8936385/SRR8936385.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: 00:10:57 27306349 reads; of these: 27306349 (100.00%) were unpaired; of these: 3071730 (11.25%) aligned 0 times 10113555 (37.04%) aligned exactly 1 time 14121064 (51.71%) aligned >1 times 88.75% overall alignment rate Time searching: 00:10:57 Overall time: 00:10:57 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] 8038844 / 24234619 = 0.3317 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 @ Tue, 30 Jun 2020 00:14:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5717025/SRX5717025.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5717025/SRX5717025.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5717025/SRX5717025.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5717025/SRX5717025.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 @ Tue, 30 Jun 2020 00:14:21: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:14:21: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:14:26: 1000000 INFO @ Tue, 30 Jun 2020 00:14:32: 2000000 INFO @ Tue, 30 Jun 2020 00:14:38: 3000000 INFO @ Tue, 30 Jun 2020 00:14:43: 4000000 INFO @ Tue, 30 Jun 2020 00:14:49: 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 @ Tue, 30 Jun 2020 00:14:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5717025/SRX5717025.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5717025/SRX5717025.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5717025/SRX5717025.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5717025/SRX5717025.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 @ Tue, 30 Jun 2020 00:14:51: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:14:51: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:14:55: 6000000 INFO @ Tue, 30 Jun 2020 00:14:56: 1000000 INFO @ Tue, 30 Jun 2020 00:15:01: 7000000 INFO @ Tue, 30 Jun 2020 00:15:01: 2000000 INFO @ Tue, 30 Jun 2020 00:15:06: 3000000 INFO @ Tue, 30 Jun 2020 00:15:07: 8000000 INFO @ Tue, 30 Jun 2020 00:15:12: 4000000 INFO @ Tue, 30 Jun 2020 00:15:13: 9000000 INFO @ Tue, 30 Jun 2020 00:15:17: 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 @ Tue, 30 Jun 2020 00:15:19: 10000000 INFO @ Tue, 30 Jun 2020 00:15:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5717025/SRX5717025.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5717025/SRX5717025.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5717025/SRX5717025.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5717025/SRX5717025.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 @ Tue, 30 Jun 2020 00:15:21: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:15:21: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:15:22: 6000000 INFO @ Tue, 30 Jun 2020 00:15:25: 11000000 INFO @ Tue, 30 Jun 2020 00:15:27: 1000000 INFO @ Tue, 30 Jun 2020 00:15:27: 7000000 INFO @ Tue, 30 Jun 2020 00:15:31: 12000000 INFO @ Tue, 30 Jun 2020 00:15:33: 2000000 INFO @ Tue, 30 Jun 2020 00:15:33: 8000000 INFO @ Tue, 30 Jun 2020 00:15:37: 13000000 INFO @ Tue, 30 Jun 2020 00:15:38: 9000000 INFO @ Tue, 30 Jun 2020 00:15:38: 3000000 INFO @ Tue, 30 Jun 2020 00:15:43: 14000000 INFO @ Tue, 30 Jun 2020 00:15:43: 10000000 INFO @ Tue, 30 Jun 2020 00:15:45: 4000000 INFO @ Tue, 30 Jun 2020 00:15:48: 11000000 INFO @ Tue, 30 Jun 2020 00:15:49: 15000000 INFO @ Tue, 30 Jun 2020 00:15:50: 5000000 INFO @ Tue, 30 Jun 2020 00:15:54: 12000000 INFO @ Tue, 30 Jun 2020 00:15:55: 16000000 INFO @ Tue, 30 Jun 2020 00:15:57: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:15:57: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:15:57: #1 total tags in treatment: 16195775 INFO @ Tue, 30 Jun 2020 00:15:57: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:15:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:15:57: 6000000 INFO @ Tue, 30 Jun 2020 00:15:57: #1 tags after filtering in treatment: 16195775 INFO @ Tue, 30 Jun 2020 00:15:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:15:57: #1 finished! INFO @ Tue, 30 Jun 2020 00:15:57: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:15:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:15:58: #2 number of paired peaks: 115 WARNING @ Tue, 30 Jun 2020 00:15:58: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Tue, 30 Jun 2020 00:15:58: start model_add_line... INFO @ Tue, 30 Jun 2020 00:15:58: start X-correlation... INFO @ Tue, 30 Jun 2020 00:15:58: end of X-cor INFO @ Tue, 30 Jun 2020 00:15:58: #2 finished! INFO @ Tue, 30 Jun 2020 00:15:58: #2 predicted fragment length is 44 bps INFO @ Tue, 30 Jun 2020 00:15:58: #2 alternative fragment length(s) may be 0,44,566 bps INFO @ Tue, 30 Jun 2020 00:15:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5717025/SRX5717025.05_model.r WARNING @ Tue, 30 Jun 2020 00:15:58: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:15:58: #2 You may need to consider one of the other alternative d(s): 0,44,566 WARNING @ Tue, 30 Jun 2020 00:15:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 00:15:58: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:15:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:15:59: 13000000 INFO @ Tue, 30 Jun 2020 00:16:03: 7000000 INFO @ Tue, 30 Jun 2020 00:16:04: 14000000 INFO @ Tue, 30 Jun 2020 00:16:09: 8000000 INFO @ Tue, 30 Jun 2020 00:16:09: 15000000 INFO @ Tue, 30 Jun 2020 00:16:15: 9000000 INFO @ Tue, 30 Jun 2020 00:16:15: 16000000 INFO @ Tue, 30 Jun 2020 00:16:16: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:16:16: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:16:16: #1 total tags in treatment: 16195775 INFO @ Tue, 30 Jun 2020 00:16:16: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:16:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:16:16: #1 tags after filtering in treatment: 16195775 INFO @ Tue, 30 Jun 2020 00:16:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:16:16: #1 finished! INFO @ Tue, 30 Jun 2020 00:16:16: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:16:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:16:17: #2 number of paired peaks: 115 WARNING @ Tue, 30 Jun 2020 00:16:17: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Tue, 30 Jun 2020 00:16:17: start model_add_line... INFO @ Tue, 30 Jun 2020 00:16:17: start X-correlation... INFO @ Tue, 30 Jun 2020 00:16:17: end of X-cor INFO @ Tue, 30 Jun 2020 00:16:17: #2 finished! INFO @ Tue, 30 Jun 2020 00:16:17: #2 predicted fragment length is 44 bps INFO @ Tue, 30 Jun 2020 00:16:17: #2 alternative fragment length(s) may be 0,44,566 bps INFO @ Tue, 30 Jun 2020 00:16:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5717025/SRX5717025.10_model.r WARNING @ Tue, 30 Jun 2020 00:16:17: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:16:17: #2 You may need to consider one of the other alternative d(s): 0,44,566 WARNING @ Tue, 30 Jun 2020 00:16:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 00:16:17: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:16:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:16:20: 10000000 INFO @ Tue, 30 Jun 2020 00:16:26: 11000000 INFO @ Tue, 30 Jun 2020 00:16:28: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 00:16:32: 12000000 INFO @ Tue, 30 Jun 2020 00:16:38: 13000000 INFO @ Tue, 30 Jun 2020 00:16:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5717025/SRX5717025.05_peaks.xls INFO @ Tue, 30 Jun 2020 00:16:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5717025/SRX5717025.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:16:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5717025/SRX5717025.05_summits.bed INFO @ Tue, 30 Jun 2020 00:16:43: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3657 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:16:44: 14000000 INFO @ Tue, 30 Jun 2020 00:16:49: 15000000 INFO @ Tue, 30 Jun 2020 00:16:49: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:16:55: 16000000 INFO @ Tue, 30 Jun 2020 00:16:56: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:16:56: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:16:56: #1 total tags in treatment: 16195775 INFO @ Tue, 30 Jun 2020 00:16:56: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:16:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:16:57: #1 tags after filtering in treatment: 16195775 INFO @ Tue, 30 Jun 2020 00:16:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:16:57: #1 finished! INFO @ Tue, 30 Jun 2020 00:16:57: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:16:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:16:58: #2 number of paired peaks: 115 WARNING @ Tue, 30 Jun 2020 00:16:58: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Tue, 30 Jun 2020 00:16:58: start model_add_line... INFO @ Tue, 30 Jun 2020 00:16:58: start X-correlation... INFO @ Tue, 30 Jun 2020 00:16:58: end of X-cor INFO @ Tue, 30 Jun 2020 00:16:58: #2 finished! INFO @ Tue, 30 Jun 2020 00:16:58: #2 predicted fragment length is 44 bps INFO @ Tue, 30 Jun 2020 00:16:58: #2 alternative fragment length(s) may be 0,44,566 bps INFO @ Tue, 30 Jun 2020 00:16:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5717025/SRX5717025.20_model.r WARNING @ Tue, 30 Jun 2020 00:16:58: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:16:58: #2 You may need to consider one of the other alternative d(s): 0,44,566 WARNING @ Tue, 30 Jun 2020 00:16:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 00:16:58: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:16:58: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 00:17:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5717025/SRX5717025.10_peaks.xls INFO @ Tue, 30 Jun 2020 00:17:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5717025/SRX5717025.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:17:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5717025/SRX5717025.10_summits.bed INFO @ Tue, 30 Jun 2020 00:17:05: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1327 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:17:27: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:17:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5717025/SRX5717025.20_peaks.xls INFO @ Tue, 30 Jun 2020 00:17:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5717025/SRX5717025.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:17:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5717025/SRX5717025.20_summits.bed INFO @ Tue, 30 Jun 2020 00:17:41: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (236 records, 4 fields): 2 millis CompletedMACS2peakCalling