Job ID = 6527494 SRX = SRX032126 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T13:51:29 prefetch.2.10.7: 1) Downloading 'SRR073952'... 2020-06-29T13:51:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:53:37 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:53:38 prefetch.2.10.7: 'SRR073952' is valid 2020-06-29T13:53:38 prefetch.2.10.7: 1) 'SRR073952' was downloaded successfully Read 27367243 spots for SRR073952/SRR073952.sra Written 27367243 spots for SRR073952/SRR073952.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: 00:05:50 27367243 reads; of these: 27367243 (100.00%) were unpaired; of these: 3527466 (12.89%) aligned 0 times 20707163 (75.66%) aligned exactly 1 time 3132614 (11.45%) aligned >1 times 87.11% overall alignment rate Time searching: 00:05:50 Overall time: 00:05:50 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 8 files... [bam_rmdupse_core] 10722735 / 23839777 = 0.4498 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 23:11:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX032126/SRX032126.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX032126/SRX032126.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX032126/SRX032126.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX032126/SRX032126.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 23:11:44: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:11:44: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:11:50: 1000000 INFO @ Mon, 29 Jun 2020 23:11:56: 2000000 INFO @ Mon, 29 Jun 2020 23:12:02: 3000000 INFO @ Mon, 29 Jun 2020 23:12:08: 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 23:12:14: 5000000 INFO @ Mon, 29 Jun 2020 23:12:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX032126/SRX032126.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX032126/SRX032126.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX032126/SRX032126.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX032126/SRX032126.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 23:12:14: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:12:14: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:12:20: 6000000 INFO @ Mon, 29 Jun 2020 23:12:21: 1000000 INFO @ Mon, 29 Jun 2020 23:12:26: 7000000 INFO @ Mon, 29 Jun 2020 23:12:28: 2000000 INFO @ Mon, 29 Jun 2020 23:12:32: 8000000 INFO @ Mon, 29 Jun 2020 23:12:34: 3000000 INFO @ Mon, 29 Jun 2020 23:12:38: 9000000 INFO @ Mon, 29 Jun 2020 23:12:41: 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 23:12:44: 10000000 INFO @ Mon, 29 Jun 2020 23:12:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX032126/SRX032126.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX032126/SRX032126.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX032126/SRX032126.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX032126/SRX032126.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 23:12:44: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:12:44: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:12:47: 5000000 INFO @ Mon, 29 Jun 2020 23:12:50: 11000000 INFO @ Mon, 29 Jun 2020 23:12:51: 1000000 INFO @ Mon, 29 Jun 2020 23:12:54: 6000000 INFO @ Mon, 29 Jun 2020 23:12:57: 12000000 INFO @ Mon, 29 Jun 2020 23:12:58: 2000000 INFO @ Mon, 29 Jun 2020 23:13:00: 7000000 INFO @ Mon, 29 Jun 2020 23:13:03: 13000000 INFO @ Mon, 29 Jun 2020 23:13:04: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 23:13:04: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 23:13:04: #1 total tags in treatment: 13117042 INFO @ Mon, 29 Jun 2020 23:13:04: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:13:04: #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 23:13:04: #1 tags after filtering in treatment: 13117042 INFO @ Mon, 29 Jun 2020 23:13:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:13:04: #1 finished! INFO @ Mon, 29 Jun 2020 23:13:04: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:13:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:13:04: 3000000 INFO @ Mon, 29 Jun 2020 23:13:05: #2 number of paired peaks: 108 WARNING @ Mon, 29 Jun 2020 23:13:05: Fewer paired peaks (108) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 108 pairs to build model! INFO @ Mon, 29 Jun 2020 23:13:05: start model_add_line... INFO @ Mon, 29 Jun 2020 23:13:05: start X-correlation... INFO @ Mon, 29 Jun 2020 23:13:05: end of X-cor INFO @ Mon, 29 Jun 2020 23:13:05: #2 finished! INFO @ Mon, 29 Jun 2020 23:13:05: #2 predicted fragment length is 44 bps INFO @ Mon, 29 Jun 2020 23:13:05: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 29 Jun 2020 23:13:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX032126/SRX032126.05_model.r WARNING @ Mon, 29 Jun 2020 23:13:05: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:13:05: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 29 Jun 2020 23:13:05: #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 23:13:05: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:13:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:13:06: 8000000 INFO @ Mon, 29 Jun 2020 23:13:10: 4000000 INFO @ Mon, 29 Jun 2020 23:13:13: 9000000 INFO @ Mon, 29 Jun 2020 23:13:16: 5000000 INFO @ Mon, 29 Jun 2020 23:13:19: 10000000 INFO @ Mon, 29 Jun 2020 23:13:22: 6000000 INFO @ Mon, 29 Jun 2020 23:13:25: 11000000 INFO @ Mon, 29 Jun 2020 23:13:28: 7000000 INFO @ Mon, 29 Jun 2020 23:13:29: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:13:32: 12000000 INFO @ Mon, 29 Jun 2020 23:13:35: 8000000 INFO @ Mon, 29 Jun 2020 23:13:38: 13000000 INFO @ Mon, 29 Jun 2020 23:13:39: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 23:13:39: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 23:13:39: #1 total tags in treatment: 13117042 INFO @ Mon, 29 Jun 2020 23:13:39: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:13:39: #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 23:13:39: #1 tags after filtering in treatment: 13117042 INFO @ Mon, 29 Jun 2020 23:13:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:13:39: #1 finished! INFO @ Mon, 29 Jun 2020 23:13:39: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:13:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:13:40: #2 number of paired peaks: 108 WARNING @ Mon, 29 Jun 2020 23:13:40: Fewer paired peaks (108) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 108 pairs to build model! INFO @ Mon, 29 Jun 2020 23:13:40: start model_add_line... INFO @ Mon, 29 Jun 2020 23:13:40: start X-correlation... INFO @ Mon, 29 Jun 2020 23:13:40: end of X-cor INFO @ Mon, 29 Jun 2020 23:13:40: #2 finished! INFO @ Mon, 29 Jun 2020 23:13:40: #2 predicted fragment length is 44 bps INFO @ Mon, 29 Jun 2020 23:13:40: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 29 Jun 2020 23:13:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX032126/SRX032126.10_model.r WARNING @ Mon, 29 Jun 2020 23:13:40: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:13:40: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 29 Jun 2020 23:13:40: #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 23:13:40: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:13:40: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:13:41: 9000000 INFO @ Mon, 29 Jun 2020 23:13:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX032126/SRX032126.05_peaks.xls INFO @ Mon, 29 Jun 2020 23:13:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX032126/SRX032126.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:13:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX032126/SRX032126.05_summits.bed INFO @ Mon, 29 Jun 2020 23:13:42: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1103 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:13:46: 10000000 INFO @ Mon, 29 Jun 2020 23:13:53: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:13:58: 12000000 INFO @ Mon, 29 Jun 2020 23:14:04: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:14:04: 13000000 INFO @ Mon, 29 Jun 2020 23:14:05: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 23:14:05: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 23:14:05: #1 total tags in treatment: 13117042 INFO @ Mon, 29 Jun 2020 23:14:05: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:14:05: #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 23:14:05: #1 tags after filtering in treatment: 13117042 INFO @ Mon, 29 Jun 2020 23:14:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:14:05: #1 finished! INFO @ Mon, 29 Jun 2020 23:14:05: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:14:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:14:06: #2 number of paired peaks: 108 WARNING @ Mon, 29 Jun 2020 23:14:06: Fewer paired peaks (108) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 108 pairs to build model! INFO @ Mon, 29 Jun 2020 23:14:06: start model_add_line... INFO @ Mon, 29 Jun 2020 23:14:06: start X-correlation... INFO @ Mon, 29 Jun 2020 23:14:06: end of X-cor INFO @ Mon, 29 Jun 2020 23:14:06: #2 finished! INFO @ Mon, 29 Jun 2020 23:14:06: #2 predicted fragment length is 44 bps INFO @ Mon, 29 Jun 2020 23:14:06: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 29 Jun 2020 23:14:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX032126/SRX032126.20_model.r WARNING @ Mon, 29 Jun 2020 23:14:06: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:14:06: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 29 Jun 2020 23:14:06: #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 23:14:06: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:14:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:14:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX032126/SRX032126.10_peaks.xls INFO @ Mon, 29 Jun 2020 23:14:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX032126/SRX032126.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:14:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX032126/SRX032126.10_summits.bed INFO @ Mon, 29 Jun 2020 23:14:17: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (578 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:14:30: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 23:14:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX032126/SRX032126.20_peaks.xls INFO @ Mon, 29 Jun 2020 23:14:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX032126/SRX032126.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:14:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX032126/SRX032126.20_summits.bed INFO @ Mon, 29 Jun 2020 23:14:43: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (389 records, 4 fields): 2 millis CompletedMACS2peakCalling