Job ID = 6627442 SRX = SRX8521382 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T02:29:02 prefetch.2.10.7: 1) Downloading 'SRR11978270'... 2020-07-14T02:29:02 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:30:28 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:30:29 prefetch.2.10.7: 'SRR11978270' is valid 2020-07-14T02:30:29 prefetch.2.10.7: 1) 'SRR11978270' was downloaded successfully 2020-07-14T02:30:29 prefetch.2.10.7: 'SRR11978270' has 0 unresolved dependencies Read 11991240 spots for SRR11978270/SRR11978270.sra Written 11991240 spots for SRR11978270/SRR11978270.sra 2020-07-14T02:31:18 prefetch.2.10.7: 1) Downloading 'SRR11978271'... 2020-07-14T02:31:18 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:32:36 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:32:37 prefetch.2.10.7: 'SRR11978271' is valid 2020-07-14T02:32:37 prefetch.2.10.7: 1) 'SRR11978271' was downloaded successfully 2020-07-14T02:32:37 prefetch.2.10.7: 'SRR11978271' has 0 unresolved dependencies Read 11899667 spots for SRR11978271/SRR11978271.sra Written 11899667 spots for SRR11978271/SRR11978271.sra 2020-07-14T02:33:40 prefetch.2.10.7: 1) Downloading 'SRR11978272'... 2020-07-14T02:33:40 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:34:58 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:34:59 prefetch.2.10.7: 'SRR11978272' is valid 2020-07-14T02:34:59 prefetch.2.10.7: 1) 'SRR11978272' was downloaded successfully 2020-07-14T02:34:59 prefetch.2.10.7: 'SRR11978272' has 0 unresolved dependencies Read 11767084 spots for SRR11978272/SRR11978272.sra Written 11767084 spots for SRR11978272/SRR11978272.sra 2020-07-14T02:35:48 prefetch.2.10.7: 1) Downloading 'SRR11978273'... 2020-07-14T02:35:48 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:37:40 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:37:40 prefetch.2.10.7: 'SRR11978273' is valid 2020-07-14T02:37:40 prefetch.2.10.7: 1) 'SRR11978273' was downloaded successfully 2020-07-14T02:37:40 prefetch.2.10.7: 'SRR11978273' has 0 unresolved dependencies Read 11903876 spots for SRR11978273/SRR11978273.sra Written 11903876 spots for SRR11978273/SRR11978273.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627637 ("srTdm6") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:20 47561867 reads; of these: 47561867 (100.00%) were unpaired; of these: 41141500 (86.50%) aligned 0 times 4285100 (9.01%) aligned exactly 1 time 2135267 (4.49%) aligned >1 times 13.50% overall alignment rate Time searching: 00:08:21 Overall time: 00:08:21 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_rmdupse_core] 1344437 / 6420367 = 0.2094 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, 14 Jul 2020 11:49:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521382/SRX8521382.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521382/SRX8521382.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521382/SRX8521382.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521382/SRX8521382.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, 14 Jul 2020 11:49:03: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:49:03: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:49:11: 1000000 INFO @ Tue, 14 Jul 2020 11:49:19: 2000000 INFO @ Tue, 14 Jul 2020 11:49:28: 3000000 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, 14 Jul 2020 11:49:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521382/SRX8521382.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521382/SRX8521382.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521382/SRX8521382.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521382/SRX8521382.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, 14 Jul 2020 11:49:33: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:49:33: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:49:36: 4000000 INFO @ Tue, 14 Jul 2020 11:49:41: 1000000 INFO @ Tue, 14 Jul 2020 11:49:45: 5000000 INFO @ Tue, 14 Jul 2020 11:49:46: #1 tag size is determined as 66 bps INFO @ Tue, 14 Jul 2020 11:49:46: #1 tag size = 66 INFO @ Tue, 14 Jul 2020 11:49:46: #1 total tags in treatment: 5075930 INFO @ Tue, 14 Jul 2020 11:49:46: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:49:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 11:49:46: #1 tags after filtering in treatment: 5075930 INFO @ Tue, 14 Jul 2020 11:49:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:49:46: #1 finished! INFO @ Tue, 14 Jul 2020 11:49:46: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:49:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:49:46: #2 number of paired peaks: 362 WARNING @ Tue, 14 Jul 2020 11:49:46: Fewer paired peaks (362) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 362 pairs to build model! INFO @ Tue, 14 Jul 2020 11:49:46: start model_add_line... INFO @ Tue, 14 Jul 2020 11:49:46: start X-correlation... INFO @ Tue, 14 Jul 2020 11:49:46: end of X-cor INFO @ Tue, 14 Jul 2020 11:49:46: #2 finished! INFO @ Tue, 14 Jul 2020 11:49:46: #2 predicted fragment length is 58 bps INFO @ Tue, 14 Jul 2020 11:49:46: #2 alternative fragment length(s) may be 58 bps INFO @ Tue, 14 Jul 2020 11:49:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521382/SRX8521382.05_model.r WARNING @ Tue, 14 Jul 2020 11:49:46: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:49:46: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Tue, 14 Jul 2020 11:49:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 11:49:46: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:49:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:49:49: 2000000 INFO @ Tue, 14 Jul 2020 11:49:56: 3000000 INFO @ Tue, 14 Jul 2020 11:49:57: #3 Call peaks for each chromosome... 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, 14 Jul 2020 11:50:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521382/SRX8521382.05_peaks.xls INFO @ Tue, 14 Jul 2020 11:50:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521382/SRX8521382.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:50:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521382/SRX8521382.05_summits.bed INFO @ Tue, 14 Jul 2020 11:50:02: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1508 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:50:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521382/SRX8521382.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521382/SRX8521382.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521382/SRX8521382.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521382/SRX8521382.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, 14 Jul 2020 11:50:03: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:50:03: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:50:03: 4000000 INFO @ Tue, 14 Jul 2020 11:50:11: 1000000 INFO @ Tue, 14 Jul 2020 11:50:11: 5000000 INFO @ Tue, 14 Jul 2020 11:50:11: #1 tag size is determined as 66 bps INFO @ Tue, 14 Jul 2020 11:50:11: #1 tag size = 66 INFO @ Tue, 14 Jul 2020 11:50:11: #1 total tags in treatment: 5075930 INFO @ Tue, 14 Jul 2020 11:50:11: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:50:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 11:50:12: #1 tags after filtering in treatment: 5075930 INFO @ Tue, 14 Jul 2020 11:50:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:50:12: #1 finished! INFO @ Tue, 14 Jul 2020 11:50:12: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:50:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:50:12: #2 number of paired peaks: 362 WARNING @ Tue, 14 Jul 2020 11:50:12: Fewer paired peaks (362) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 362 pairs to build model! INFO @ Tue, 14 Jul 2020 11:50:12: start model_add_line... INFO @ Tue, 14 Jul 2020 11:50:12: start X-correlation... INFO @ Tue, 14 Jul 2020 11:50:12: end of X-cor INFO @ Tue, 14 Jul 2020 11:50:12: #2 finished! INFO @ Tue, 14 Jul 2020 11:50:12: #2 predicted fragment length is 58 bps INFO @ Tue, 14 Jul 2020 11:50:12: #2 alternative fragment length(s) may be 58 bps INFO @ Tue, 14 Jul 2020 11:50:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521382/SRX8521382.10_model.r WARNING @ Tue, 14 Jul 2020 11:50:12: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:50:12: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Tue, 14 Jul 2020 11:50:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 11:50:12: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:50:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:50:18: 2000000 INFO @ Tue, 14 Jul 2020 11:50:23: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:50:25: 3000000 INFO @ Tue, 14 Jul 2020 11:50:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521382/SRX8521382.10_peaks.xls INFO @ Tue, 14 Jul 2020 11:50:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521382/SRX8521382.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:50:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521382/SRX8521382.10_summits.bed INFO @ Tue, 14 Jul 2020 11:50:28: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (800 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 11:50:32: 4000000 INFO @ Tue, 14 Jul 2020 11:50:39: 5000000 INFO @ Tue, 14 Jul 2020 11:50:39: #1 tag size is determined as 66 bps INFO @ Tue, 14 Jul 2020 11:50:39: #1 tag size = 66 INFO @ Tue, 14 Jul 2020 11:50:39: #1 total tags in treatment: 5075930 INFO @ Tue, 14 Jul 2020 11:50:39: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:50:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 11:50:39: #1 tags after filtering in treatment: 5075930 INFO @ Tue, 14 Jul 2020 11:50:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:50:39: #1 finished! INFO @ Tue, 14 Jul 2020 11:50:39: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:50:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:50:40: #2 number of paired peaks: 362 WARNING @ Tue, 14 Jul 2020 11:50:40: Fewer paired peaks (362) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 362 pairs to build model! INFO @ Tue, 14 Jul 2020 11:50:40: start model_add_line... INFO @ Tue, 14 Jul 2020 11:50:40: start X-correlation... INFO @ Tue, 14 Jul 2020 11:50:40: end of X-cor INFO @ Tue, 14 Jul 2020 11:50:40: #2 finished! INFO @ Tue, 14 Jul 2020 11:50:40: #2 predicted fragment length is 58 bps INFO @ Tue, 14 Jul 2020 11:50:40: #2 alternative fragment length(s) may be 58 bps INFO @ Tue, 14 Jul 2020 11:50:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521382/SRX8521382.20_model.r WARNING @ Tue, 14 Jul 2020 11:50:40: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:50:40: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Tue, 14 Jul 2020 11:50:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 11:50:40: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:50:40: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 11:50:50: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:50:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521382/SRX8521382.20_peaks.xls INFO @ Tue, 14 Jul 2020 11:50:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521382/SRX8521382.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:50:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521382/SRX8521382.20_summits.bed INFO @ Tue, 14 Jul 2020 11:50:56: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (324 records, 4 fields): 2 millis CompletedMACS2peakCalling