Job ID = 6528158 SRX = SRX4923196 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T14:48:40 prefetch.2.10.7: 1) Downloading 'SRR8096346'... 2020-06-29T14:48:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:49:49 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:49:49 prefetch.2.10.7: 'SRR8096346' is valid 2020-06-29T14:49:49 prefetch.2.10.7: 1) 'SRR8096346' was downloaded successfully 2020-06-29T14:49:49 prefetch.2.10.7: 'SRR8096346' has 0 unresolved dependencies Read 25358795 spots for SRR8096346/SRR8096346.sra Written 25358795 spots for SRR8096346/SRR8096346.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:00 25358795 reads; of these: 25358795 (100.00%) were unpaired; of these: 714970 (2.82%) aligned 0 times 19546676 (77.08%) aligned exactly 1 time 5097149 (20.10%) aligned >1 times 97.18% overall alignment rate Time searching: 00:07:01 Overall time: 00:07:01 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] 6315238 / 24643825 = 0.2563 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 00:10:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4923196/SRX4923196.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4923196/SRX4923196.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4923196/SRX4923196.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4923196/SRX4923196.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 00:10:35: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:10:35: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:10:40: 1000000 INFO @ Tue, 30 Jun 2020 00:10:46: 2000000 INFO @ Tue, 30 Jun 2020 00:10:51: 3000000 INFO @ Tue, 30 Jun 2020 00:10:57: 4000000 INFO @ Tue, 30 Jun 2020 00:11:02: 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 00:11:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4923196/SRX4923196.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4923196/SRX4923196.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4923196/SRX4923196.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4923196/SRX4923196.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 00:11:05: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:11:05: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:11:08: 6000000 INFO @ Tue, 30 Jun 2020 00:11:11: 1000000 INFO @ Tue, 30 Jun 2020 00:11:14: 7000000 INFO @ Tue, 30 Jun 2020 00:11:17: 2000000 INFO @ Tue, 30 Jun 2020 00:11:20: 8000000 INFO @ Tue, 30 Jun 2020 00:11:23: 3000000 INFO @ Tue, 30 Jun 2020 00:11:26: 9000000 INFO @ Tue, 30 Jun 2020 00:11:29: 4000000 INFO @ Tue, 30 Jun 2020 00:11:32: 10000000 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 00:11:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4923196/SRX4923196.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4923196/SRX4923196.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4923196/SRX4923196.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4923196/SRX4923196.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 00:11:35: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:11:35: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:11:35: 5000000 INFO @ Tue, 30 Jun 2020 00:11:38: 11000000 INFO @ Tue, 30 Jun 2020 00:11:40: 1000000 INFO @ Tue, 30 Jun 2020 00:11:41: 6000000 INFO @ Tue, 30 Jun 2020 00:11:44: 12000000 INFO @ Tue, 30 Jun 2020 00:11:46: 2000000 INFO @ Tue, 30 Jun 2020 00:11:47: 7000000 INFO @ Tue, 30 Jun 2020 00:11:50: 13000000 INFO @ Tue, 30 Jun 2020 00:11:52: 3000000 INFO @ Tue, 30 Jun 2020 00:11:53: 8000000 INFO @ Tue, 30 Jun 2020 00:11:56: 14000000 INFO @ Tue, 30 Jun 2020 00:11:58: 4000000 INFO @ Tue, 30 Jun 2020 00:11:58: 9000000 INFO @ Tue, 30 Jun 2020 00:12:02: 15000000 INFO @ Tue, 30 Jun 2020 00:12:04: 5000000 INFO @ Tue, 30 Jun 2020 00:12:04: 10000000 INFO @ Tue, 30 Jun 2020 00:12:07: 16000000 INFO @ Tue, 30 Jun 2020 00:12:10: 6000000 INFO @ Tue, 30 Jun 2020 00:12:10: 11000000 INFO @ Tue, 30 Jun 2020 00:12:13: 17000000 INFO @ Tue, 30 Jun 2020 00:12:16: 12000000 INFO @ Tue, 30 Jun 2020 00:12:16: 7000000 INFO @ Tue, 30 Jun 2020 00:12:19: 18000000 INFO @ Tue, 30 Jun 2020 00:12:21: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:12:21: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:12:21: #1 total tags in treatment: 18328587 INFO @ Tue, 30 Jun 2020 00:12:21: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:12:21: #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 00:12:21: #1 tags after filtering in treatment: 18328587 INFO @ Tue, 30 Jun 2020 00:12:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:12:21: #1 finished! INFO @ Tue, 30 Jun 2020 00:12:21: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:12:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:12:22: 13000000 INFO @ Tue, 30 Jun 2020 00:12:22: 8000000 INFO @ Tue, 30 Jun 2020 00:12:23: #2 number of paired peaks: 169 WARNING @ Tue, 30 Jun 2020 00:12:23: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Tue, 30 Jun 2020 00:12:23: start model_add_line... INFO @ Tue, 30 Jun 2020 00:12:23: start X-correlation... INFO @ Tue, 30 Jun 2020 00:12:23: end of X-cor INFO @ Tue, 30 Jun 2020 00:12:23: #2 finished! INFO @ Tue, 30 Jun 2020 00:12:23: #2 predicted fragment length is 48 bps INFO @ Tue, 30 Jun 2020 00:12:23: #2 alternative fragment length(s) may be 1,48,511,530,583 bps INFO @ Tue, 30 Jun 2020 00:12:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4923196/SRX4923196.05_model.r WARNING @ Tue, 30 Jun 2020 00:12:23: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:12:23: #2 You may need to consider one of the other alternative d(s): 1,48,511,530,583 WARNING @ Tue, 30 Jun 2020 00:12:23: #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 00:12:23: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:12:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:12:27: 14000000 INFO @ Tue, 30 Jun 2020 00:12:28: 9000000 INFO @ Tue, 30 Jun 2020 00:12:32: 15000000 INFO @ Tue, 30 Jun 2020 00:12:34: 10000000 INFO @ Tue, 30 Jun 2020 00:12:37: 16000000 INFO @ Tue, 30 Jun 2020 00:12:39: 11000000 INFO @ Tue, 30 Jun 2020 00:12:43: 17000000 INFO @ Tue, 30 Jun 2020 00:12:45: 12000000 INFO @ Tue, 30 Jun 2020 00:12:48: 18000000 INFO @ Tue, 30 Jun 2020 00:12:50: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:12:50: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:12:50: #1 total tags in treatment: 18328587 INFO @ Tue, 30 Jun 2020 00:12:50: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:12:50: #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 00:12:50: #1 tags after filtering in treatment: 18328587 INFO @ Tue, 30 Jun 2020 00:12:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:12:50: #1 finished! INFO @ Tue, 30 Jun 2020 00:12:50: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:12:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:12:51: 13000000 INFO @ Tue, 30 Jun 2020 00:12:51: #2 number of paired peaks: 169 WARNING @ Tue, 30 Jun 2020 00:12:51: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Tue, 30 Jun 2020 00:12:51: start model_add_line... INFO @ Tue, 30 Jun 2020 00:12:51: start X-correlation... INFO @ Tue, 30 Jun 2020 00:12:51: end of X-cor INFO @ Tue, 30 Jun 2020 00:12:51: #2 finished! INFO @ Tue, 30 Jun 2020 00:12:51: #2 predicted fragment length is 48 bps INFO @ Tue, 30 Jun 2020 00:12:51: #2 alternative fragment length(s) may be 1,48,511,530,583 bps INFO @ Tue, 30 Jun 2020 00:12:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4923196/SRX4923196.10_model.r WARNING @ Tue, 30 Jun 2020 00:12:51: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:12:51: #2 You may need to consider one of the other alternative d(s): 1,48,511,530,583 WARNING @ Tue, 30 Jun 2020 00:12:51: #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 00:12:51: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:12:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:12:53: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:12:57: 14000000 INFO @ Tue, 30 Jun 2020 00:13:02: 15000000 INFO @ Tue, 30 Jun 2020 00:13:08: 16000000 INFO @ Tue, 30 Jun 2020 00:13:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4923196/SRX4923196.05_peaks.xls INFO @ Tue, 30 Jun 2020 00:13:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4923196/SRX4923196.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:13:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4923196/SRX4923196.05_summits.bed INFO @ Tue, 30 Jun 2020 00:13:08: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (367 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:13:13: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 00:13:19: 18000000 INFO @ Tue, 30 Jun 2020 00:13:21: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:13:21: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:13:21: #1 total tags in treatment: 18328587 INFO @ Tue, 30 Jun 2020 00:13:21: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:13:21: #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 00:13:21: #1 tags after filtering in treatment: 18328587 INFO @ Tue, 30 Jun 2020 00:13:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:13:21: #1 finished! INFO @ Tue, 30 Jun 2020 00:13:21: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:13:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:13:22: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:13:22: #2 number of paired peaks: 169 WARNING @ Tue, 30 Jun 2020 00:13:22: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Tue, 30 Jun 2020 00:13:22: start model_add_line... INFO @ Tue, 30 Jun 2020 00:13:22: start X-correlation... INFO @ Tue, 30 Jun 2020 00:13:22: end of X-cor INFO @ Tue, 30 Jun 2020 00:13:22: #2 finished! INFO @ Tue, 30 Jun 2020 00:13:22: #2 predicted fragment length is 48 bps INFO @ Tue, 30 Jun 2020 00:13:22: #2 alternative fragment length(s) may be 1,48,511,530,583 bps INFO @ Tue, 30 Jun 2020 00:13:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4923196/SRX4923196.20_model.r WARNING @ Tue, 30 Jun 2020 00:13:22: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:13:22: #2 You may need to consider one of the other alternative d(s): 1,48,511,530,583 WARNING @ Tue, 30 Jun 2020 00:13:22: #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 00:13:22: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:13:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:13:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4923196/SRX4923196.10_peaks.xls INFO @ Tue, 30 Jun 2020 00:13:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4923196/SRX4923196.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:13:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4923196/SRX4923196.10_summits.bed INFO @ Tue, 30 Jun 2020 00:13:37: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (223 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:13:53: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 00:14:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4923196/SRX4923196.20_peaks.xls INFO @ Tue, 30 Jun 2020 00:14:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4923196/SRX4923196.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:14:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4923196/SRX4923196.20_summits.bed INFO @ Tue, 30 Jun 2020 00:14:09: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (87 records, 4 fields): 2 millis CompletedMACS2peakCalling