Job ID = 6527780 SRX = SRX287581 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T13:51:15 prefetch.2.10.7: 1) Downloading 'SRR869724'... 2020-06-29T13:51:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:54:49 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:54:49 prefetch.2.10.7: 1) 'SRR869724' was downloaded successfully Read 22735312 spots for SRR869724/SRR869724.sra Written 22735312 spots for SRR869724/SRR869724.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: 00:08:23 22735312 reads; of these: 22735312 (100.00%) were unpaired; of these: 857331 (3.77%) aligned 0 times 15851328 (69.72%) aligned exactly 1 time 6026653 (26.51%) aligned >1 times 96.23% overall alignment rate Time searching: 00:08:23 Overall time: 00:08:23 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] 2592543 / 21877981 = 0.1185 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 @ Mon, 29 Jun 2020 23:18:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287581/SRX287581.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287581/SRX287581.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287581/SRX287581.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287581/SRX287581.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 @ Mon, 29 Jun 2020 23:18:30: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:18:30: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:18:36: 1000000 INFO @ Mon, 29 Jun 2020 23:18:42: 2000000 INFO @ Mon, 29 Jun 2020 23:18:48: 3000000 INFO @ Mon, 29 Jun 2020 23:18:54: 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 @ Mon, 29 Jun 2020 23:19:00: 5000000 INFO @ Mon, 29 Jun 2020 23:19:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287581/SRX287581.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287581/SRX287581.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287581/SRX287581.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287581/SRX287581.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 @ Mon, 29 Jun 2020 23:19:00: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:19:00: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:19:06: 6000000 INFO @ Mon, 29 Jun 2020 23:19:06: 1000000 INFO @ Mon, 29 Jun 2020 23:19:13: 7000000 INFO @ Mon, 29 Jun 2020 23:19:13: 2000000 INFO @ Mon, 29 Jun 2020 23:19:19: 8000000 INFO @ Mon, 29 Jun 2020 23:19:19: 3000000 INFO @ Mon, 29 Jun 2020 23:19:25: 9000000 INFO @ Mon, 29 Jun 2020 23:19:25: 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 @ Mon, 29 Jun 2020 23:19:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287581/SRX287581.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287581/SRX287581.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287581/SRX287581.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287581/SRX287581.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 @ Mon, 29 Jun 2020 23:19:30: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:19:30: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:19:32: 5000000 INFO @ Mon, 29 Jun 2020 23:19:32: 10000000 INFO @ Mon, 29 Jun 2020 23:19:37: 1000000 INFO @ Mon, 29 Jun 2020 23:19:38: 6000000 INFO @ Mon, 29 Jun 2020 23:19:38: 11000000 INFO @ Mon, 29 Jun 2020 23:19:43: 2000000 INFO @ Mon, 29 Jun 2020 23:19:44: 7000000 INFO @ Mon, 29 Jun 2020 23:19:44: 12000000 INFO @ Mon, 29 Jun 2020 23:19:49: 3000000 INFO @ Mon, 29 Jun 2020 23:19:51: 8000000 INFO @ Mon, 29 Jun 2020 23:19:51: 13000000 INFO @ Mon, 29 Jun 2020 23:19:56: 4000000 INFO @ Mon, 29 Jun 2020 23:19:57: 9000000 INFO @ Mon, 29 Jun 2020 23:19:57: 14000000 INFO @ Mon, 29 Jun 2020 23:20:02: 5000000 INFO @ Mon, 29 Jun 2020 23:20:03: 10000000 INFO @ Mon, 29 Jun 2020 23:20:04: 15000000 INFO @ Mon, 29 Jun 2020 23:20:08: 6000000 INFO @ Mon, 29 Jun 2020 23:20:10: 11000000 INFO @ Mon, 29 Jun 2020 23:20:10: 16000000 INFO @ Mon, 29 Jun 2020 23:20:14: 7000000 INFO @ Mon, 29 Jun 2020 23:20:16: 12000000 INFO @ Mon, 29 Jun 2020 23:20:16: 17000000 INFO @ Mon, 29 Jun 2020 23:20:20: 8000000 INFO @ Mon, 29 Jun 2020 23:20:22: 13000000 INFO @ Mon, 29 Jun 2020 23:20:22: 18000000 INFO @ Mon, 29 Jun 2020 23:20:26: 9000000 INFO @ Mon, 29 Jun 2020 23:20:28: 14000000 INFO @ Mon, 29 Jun 2020 23:20:28: 19000000 INFO @ Mon, 29 Jun 2020 23:20:30: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:20:30: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:20:30: #1 total tags in treatment: 19285438 INFO @ Mon, 29 Jun 2020 23:20:30: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:20:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:20:31: #1 tags after filtering in treatment: 19285438 INFO @ Mon, 29 Jun 2020 23:20:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:20:31: #1 finished! INFO @ Mon, 29 Jun 2020 23:20:31: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:20:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:20:32: #2 number of paired peaks: 201 WARNING @ Mon, 29 Jun 2020 23:20:32: Fewer paired peaks (201) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 201 pairs to build model! INFO @ Mon, 29 Jun 2020 23:20:32: start model_add_line... INFO @ Mon, 29 Jun 2020 23:20:32: start X-correlation... INFO @ Mon, 29 Jun 2020 23:20:32: end of X-cor INFO @ Mon, 29 Jun 2020 23:20:32: #2 finished! INFO @ Mon, 29 Jun 2020 23:20:32: #2 predicted fragment length is 48 bps INFO @ Mon, 29 Jun 2020 23:20:32: #2 alternative fragment length(s) may be 48 bps INFO @ Mon, 29 Jun 2020 23:20:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287581/SRX287581.05_model.r WARNING @ Mon, 29 Jun 2020 23:20:32: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:20:32: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Mon, 29 Jun 2020 23:20:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:20:32: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:20:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:20:32: 10000000 INFO @ Mon, 29 Jun 2020 23:20:34: 15000000 INFO @ Mon, 29 Jun 2020 23:20:38: 11000000 INFO @ Mon, 29 Jun 2020 23:20:40: 16000000 INFO @ Mon, 29 Jun 2020 23:20:45: 12000000 INFO @ Mon, 29 Jun 2020 23:20:45: 17000000 INFO @ Mon, 29 Jun 2020 23:20:51: 13000000 INFO @ Mon, 29 Jun 2020 23:20:51: 18000000 INFO @ Mon, 29 Jun 2020 23:20:56: 19000000 INFO @ Mon, 29 Jun 2020 23:20:57: 14000000 INFO @ Mon, 29 Jun 2020 23:20:58: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:20:58: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:20:58: #1 total tags in treatment: 19285438 INFO @ Mon, 29 Jun 2020 23:20:58: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:20:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:20:59: #1 tags after filtering in treatment: 19285438 INFO @ Mon, 29 Jun 2020 23:20:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:20:59: #1 finished! INFO @ Mon, 29 Jun 2020 23:20:59: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:20:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:21:00: #2 number of paired peaks: 201 WARNING @ Mon, 29 Jun 2020 23:21:00: Fewer paired peaks (201) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 201 pairs to build model! INFO @ Mon, 29 Jun 2020 23:21:00: start model_add_line... INFO @ Mon, 29 Jun 2020 23:21:00: start X-correlation... INFO @ Mon, 29 Jun 2020 23:21:00: end of X-cor INFO @ Mon, 29 Jun 2020 23:21:00: #2 finished! INFO @ Mon, 29 Jun 2020 23:21:00: #2 predicted fragment length is 48 bps INFO @ Mon, 29 Jun 2020 23:21:00: #2 alternative fragment length(s) may be 48 bps INFO @ Mon, 29 Jun 2020 23:21:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287581/SRX287581.10_model.r WARNING @ Mon, 29 Jun 2020 23:21:00: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:21:00: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Mon, 29 Jun 2020 23:21:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:21:00: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:21:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:21:03: 15000000 INFO @ Mon, 29 Jun 2020 23:21:05: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:21:09: 16000000 INFO @ Mon, 29 Jun 2020 23:21:15: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:21:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287581/SRX287581.05_peaks.xls INFO @ Mon, 29 Jun 2020 23:21:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287581/SRX287581.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:21:21: 18000000 INFO @ Mon, 29 Jun 2020 23:21:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287581/SRX287581.05_summits.bed INFO @ Mon, 29 Jun 2020 23:21:22: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2047 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:21:27: 19000000 INFO @ Mon, 29 Jun 2020 23:21:29: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:21:29: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:21:29: #1 total tags in treatment: 19285438 INFO @ Mon, 29 Jun 2020 23:21:29: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:21:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:21:29: #1 tags after filtering in treatment: 19285438 INFO @ Mon, 29 Jun 2020 23:21:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:21:29: #1 finished! INFO @ Mon, 29 Jun 2020 23:21:29: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:21:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:21:31: #2 number of paired peaks: 201 WARNING @ Mon, 29 Jun 2020 23:21:31: Fewer paired peaks (201) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 201 pairs to build model! INFO @ Mon, 29 Jun 2020 23:21:31: start model_add_line... INFO @ Mon, 29 Jun 2020 23:21:31: start X-correlation... INFO @ Mon, 29 Jun 2020 23:21:31: end of X-cor INFO @ Mon, 29 Jun 2020 23:21:31: #2 finished! INFO @ Mon, 29 Jun 2020 23:21:31: #2 predicted fragment length is 48 bps INFO @ Mon, 29 Jun 2020 23:21:31: #2 alternative fragment length(s) may be 48 bps INFO @ Mon, 29 Jun 2020 23:21:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287581/SRX287581.20_model.r WARNING @ Mon, 29 Jun 2020 23:21:31: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:21:31: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Mon, 29 Jun 2020 23:21:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:21:31: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:21:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:21:33: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:21:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287581/SRX287581.10_peaks.xls INFO @ Mon, 29 Jun 2020 23:21:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287581/SRX287581.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:21:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287581/SRX287581.10_summits.bed INFO @ Mon, 29 Jun 2020 23:21:49: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1631 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:22:04: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 23:22:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287581/SRX287581.20_peaks.xls INFO @ Mon, 29 Jun 2020 23:22:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287581/SRX287581.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:22:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287581/SRX287581.20_summits.bed INFO @ Mon, 29 Jun 2020 23:22:20: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (1193 records, 4 fields): 4 millis CompletedMACS2peakCalling