Job ID = 6508795 SRX = SRX485218 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T14:53:37 prefetch.2.10.7: 1) Downloading 'SRR1187976'... 2020-06-26T14:53:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:55:47 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:55:47 prefetch.2.10.7: 1) 'SRR1187976' was downloaded successfully 2020-06-26T14:55:47 prefetch.2.10.7: 'SRR1187976' has 0 unresolved dependencies Read 21943222 spots for SRR1187976/SRR1187976.sra Written 21943222 spots for SRR1187976/SRR1187976.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:04 21943222 reads; of these: 21943222 (100.00%) were unpaired; of these: 962613 (4.39%) aligned 0 times 11175605 (50.93%) aligned exactly 1 time 9805004 (44.68%) aligned >1 times 95.61% overall alignment rate Time searching: 00:07:05 Overall time: 00:07:05 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 12 files... [bam_rmdupse_core] 4873661 / 20980609 = 0.2323 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 @ Sat, 27 Jun 2020 00:09:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX485218/SRX485218.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX485218/SRX485218.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX485218/SRX485218.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX485218/SRX485218.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 @ Sat, 27 Jun 2020 00:09:55: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:09:55: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:10:00: 1000000 INFO @ Sat, 27 Jun 2020 00:10:05: 2000000 INFO @ Sat, 27 Jun 2020 00:10:10: 3000000 INFO @ Sat, 27 Jun 2020 00:10:15: 4000000 INFO @ Sat, 27 Jun 2020 00:10:20: 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 @ Sat, 27 Jun 2020 00:10:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX485218/SRX485218.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX485218/SRX485218.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX485218/SRX485218.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX485218/SRX485218.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 @ Sat, 27 Jun 2020 00:10:25: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:10:25: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:10:25: 6000000 INFO @ Sat, 27 Jun 2020 00:10:30: 1000000 INFO @ Sat, 27 Jun 2020 00:10:30: 7000000 INFO @ Sat, 27 Jun 2020 00:10:35: 8000000 INFO @ Sat, 27 Jun 2020 00:10:35: 2000000 INFO @ Sat, 27 Jun 2020 00:10:40: 9000000 INFO @ Sat, 27 Jun 2020 00:10:40: 3000000 INFO @ Sat, 27 Jun 2020 00:10:45: 10000000 INFO @ Sat, 27 Jun 2020 00:10:45: 4000000 INFO @ Sat, 27 Jun 2020 00:10:50: 11000000 INFO @ Sat, 27 Jun 2020 00:10:50: 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 @ Sat, 27 Jun 2020 00:10:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX485218/SRX485218.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX485218/SRX485218.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX485218/SRX485218.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX485218/SRX485218.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 @ Sat, 27 Jun 2020 00:10:55: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:10:55: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:10:55: 12000000 INFO @ Sat, 27 Jun 2020 00:10:55: 6000000 INFO @ Sat, 27 Jun 2020 00:11:00: 7000000 INFO @ Sat, 27 Jun 2020 00:11:00: 13000000 INFO @ Sat, 27 Jun 2020 00:11:01: 1000000 INFO @ Sat, 27 Jun 2020 00:11:05: 8000000 INFO @ Sat, 27 Jun 2020 00:11:06: 14000000 INFO @ Sat, 27 Jun 2020 00:11:07: 2000000 INFO @ Sat, 27 Jun 2020 00:11:10: 9000000 INFO @ Sat, 27 Jun 2020 00:11:11: 15000000 INFO @ Sat, 27 Jun 2020 00:11:13: 3000000 INFO @ Sat, 27 Jun 2020 00:11:16: 10000000 INFO @ Sat, 27 Jun 2020 00:11:16: 16000000 INFO @ Sat, 27 Jun 2020 00:11:17: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 00:11:17: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 00:11:17: #1 total tags in treatment: 16106948 INFO @ Sat, 27 Jun 2020 00:11:17: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:11:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:11:18: #1 tags after filtering in treatment: 16106920 INFO @ Sat, 27 Jun 2020 00:11:18: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:11:18: #1 finished! INFO @ Sat, 27 Jun 2020 00:11:18: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:11:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:11:19: #2 number of paired peaks: 1488 INFO @ Sat, 27 Jun 2020 00:11:19: start model_add_line... INFO @ Sat, 27 Jun 2020 00:11:19: start X-correlation... INFO @ Sat, 27 Jun 2020 00:11:19: 4000000 INFO @ Sat, 27 Jun 2020 00:11:19: end of X-cor INFO @ Sat, 27 Jun 2020 00:11:19: #2 finished! INFO @ Sat, 27 Jun 2020 00:11:19: #2 predicted fragment length is 45 bps INFO @ Sat, 27 Jun 2020 00:11:19: #2 alternative fragment length(s) may be 2,45,596 bps INFO @ Sat, 27 Jun 2020 00:11:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX485218/SRX485218.05_model.r WARNING @ Sat, 27 Jun 2020 00:11:19: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:11:19: #2 You may need to consider one of the other alternative d(s): 2,45,596 WARNING @ Sat, 27 Jun 2020 00:11:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:11:19: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:11:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:11:21: 11000000 INFO @ Sat, 27 Jun 2020 00:11:25: 5000000 INFO @ Sat, 27 Jun 2020 00:11:26: 12000000 INFO @ Sat, 27 Jun 2020 00:11:30: 6000000 INFO @ Sat, 27 Jun 2020 00:11:31: 13000000 INFO @ Sat, 27 Jun 2020 00:11:36: 7000000 INFO @ Sat, 27 Jun 2020 00:11:37: 14000000 INFO @ Sat, 27 Jun 2020 00:11:41: 8000000 INFO @ Sat, 27 Jun 2020 00:11:42: 15000000 INFO @ Sat, 27 Jun 2020 00:11:46: 9000000 INFO @ Sat, 27 Jun 2020 00:11:47: 16000000 INFO @ Sat, 27 Jun 2020 00:11:48: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 00:11:48: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 00:11:48: #1 total tags in treatment: 16106948 INFO @ Sat, 27 Jun 2020 00:11:48: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:11:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:11:48: #1 tags after filtering in treatment: 16106920 INFO @ Sat, 27 Jun 2020 00:11:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:11:48: #1 finished! INFO @ Sat, 27 Jun 2020 00:11:48: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:11:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:11:50: #2 number of paired peaks: 1488 INFO @ Sat, 27 Jun 2020 00:11:50: start model_add_line... INFO @ Sat, 27 Jun 2020 00:11:50: start X-correlation... INFO @ Sat, 27 Jun 2020 00:11:50: end of X-cor INFO @ Sat, 27 Jun 2020 00:11:50: #2 finished! INFO @ Sat, 27 Jun 2020 00:11:50: #2 predicted fragment length is 45 bps INFO @ Sat, 27 Jun 2020 00:11:50: #2 alternative fragment length(s) may be 2,45,596 bps INFO @ Sat, 27 Jun 2020 00:11:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX485218/SRX485218.10_model.r WARNING @ Sat, 27 Jun 2020 00:11:50: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:11:50: #2 You may need to consider one of the other alternative d(s): 2,45,596 WARNING @ Sat, 27 Jun 2020 00:11:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:11:50: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:11:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:11:51: 10000000 INFO @ Sat, 27 Jun 2020 00:11:51: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:11:56: 11000000 INFO @ Sat, 27 Jun 2020 00:12:01: 12000000 INFO @ Sat, 27 Jun 2020 00:12:07: 13000000 INFO @ Sat, 27 Jun 2020 00:12:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX485218/SRX485218.05_peaks.xls INFO @ Sat, 27 Jun 2020 00:12:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX485218/SRX485218.05_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:12:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX485218/SRX485218.05_summits.bed INFO @ Sat, 27 Jun 2020 00:12:07: Done! pass1 - making usageList (800 chroms): 1 millis pass2 - checking and writing primary data (3694 records, 4 fields): 32 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 27 Jun 2020 00:12:12: 14000000 INFO @ Sat, 27 Jun 2020 00:12:17: 15000000 INFO @ Sat, 27 Jun 2020 00:12:23: 16000000 INFO @ Sat, 27 Jun 2020 00:12:23: #1 tag size is determined as 50 bps INFO @ Sat, 27 Jun 2020 00:12:23: #1 tag size = 50 INFO @ Sat, 27 Jun 2020 00:12:23: #1 total tags in treatment: 16106948 INFO @ Sat, 27 Jun 2020 00:12:23: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:12:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:12:24: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:12:24: #1 tags after filtering in treatment: 16106920 INFO @ Sat, 27 Jun 2020 00:12:24: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:12:24: #1 finished! INFO @ Sat, 27 Jun 2020 00:12:24: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:12:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:12:25: #2 number of paired peaks: 1488 INFO @ Sat, 27 Jun 2020 00:12:25: start model_add_line... INFO @ Sat, 27 Jun 2020 00:12:25: start X-correlation... INFO @ Sat, 27 Jun 2020 00:12:25: end of X-cor INFO @ Sat, 27 Jun 2020 00:12:25: #2 finished! INFO @ Sat, 27 Jun 2020 00:12:25: #2 predicted fragment length is 45 bps INFO @ Sat, 27 Jun 2020 00:12:25: #2 alternative fragment length(s) may be 2,45,596 bps INFO @ Sat, 27 Jun 2020 00:12:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX485218/SRX485218.20_model.r WARNING @ Sat, 27 Jun 2020 00:12:25: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:12:25: #2 You may need to consider one of the other alternative d(s): 2,45,596 WARNING @ Sat, 27 Jun 2020 00:12:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:12:25: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:12:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:12:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX485218/SRX485218.10_peaks.xls INFO @ Sat, 27 Jun 2020 00:12:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX485218/SRX485218.10_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:12:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX485218/SRX485218.10_summits.bed INFO @ Sat, 27 Jun 2020 00:12:40: Done! pass1 - making usageList (651 chroms): 2 millis pass2 - checking and writing primary data (2456 records, 4 fields): 21 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 27 Jun 2020 00:12:59: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:13:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX485218/SRX485218.20_peaks.xls INFO @ Sat, 27 Jun 2020 00:13:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX485218/SRX485218.20_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:13:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX485218/SRX485218.20_summits.bed INFO @ Sat, 27 Jun 2020 00:13:16: Done! pass1 - making usageList (489 chroms): 1 millis pass2 - checking and writing primary data (1702 records, 4 fields): 16 millis CompletedMACS2peakCalling