Job ID = 6627284 SRX = SRX8521348 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T01:50:11 prefetch.2.10.7: 1) Downloading 'SRR11978636'... 2020-07-14T01:50:11 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:51:24 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:51:24 prefetch.2.10.7: 'SRR11978636' is valid 2020-07-14T01:51:24 prefetch.2.10.7: 1) 'SRR11978636' was downloaded successfully 2020-07-14T01:51:24 prefetch.2.10.7: 'SRR11978636' has 0 unresolved dependencies Read 11895039 spots for SRR11978636/SRR11978636.sra Written 11895039 spots for SRR11978636/SRR11978636.sra 2020-07-14T01:52:19 prefetch.2.10.7: 1) Downloading 'SRR11978637'... 2020-07-14T01:52:19 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:53:13 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:53:13 prefetch.2.10.7: 'SRR11978637' is valid 2020-07-14T01:53:13 prefetch.2.10.7: 1) 'SRR11978637' was downloaded successfully 2020-07-14T01:53:13 prefetch.2.10.7: 'SRR11978637' has 0 unresolved dependencies Read 11608603 spots for SRR11978637/SRR11978637.sra Written 11608603 spots for SRR11978637/SRR11978637.sra 2020-07-14T01:54:29 prefetch.2.10.7: 1) Downloading 'SRR11978638'... 2020-07-14T01:54:29 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:55:50 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:55:51 prefetch.2.10.7: 'SRR11978638' is valid 2020-07-14T01:55:51 prefetch.2.10.7: 1) 'SRR11978638' was downloaded successfully 2020-07-14T01:55:51 prefetch.2.10.7: 'SRR11978638' has 0 unresolved dependencies Read 12009293 spots for SRR11978638/SRR11978638.sra Written 12009293 spots for SRR11978638/SRR11978638.sra 2020-07-14T01:56:44 prefetch.2.10.7: 1) Downloading 'SRR11978639'... 2020-07-14T01:56:44 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:59:47 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:59:47 prefetch.2.10.7: 'SRR11978639' is valid 2020-07-14T01:59:47 prefetch.2.10.7: 1) 'SRR11978639' was downloaded successfully 2020-07-14T01:59:47 prefetch.2.10.7: 'SRR11978639' has 0 unresolved dependencies Read 12007184 spots for SRR11978639/SRR11978639.sra Written 12007184 spots for SRR11978639/SRR11978639.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627518 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:06 47520119 reads; of these: 47520119 (100.00%) were unpaired; of these: 41860907 (88.09%) aligned 0 times 4422269 (9.31%) aligned exactly 1 time 1236943 (2.60%) aligned >1 times 11.91% overall alignment rate Time searching: 00:07:06 Overall time: 00:07:06 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] 1521345 / 5659212 = 0.2688 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 11:09:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521348/SRX8521348.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521348/SRX8521348.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521348/SRX8521348.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521348/SRX8521348.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 11:09:53: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:09:53: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:09:59: 1000000 INFO @ Tue, 14 Jul 2020 11:10:05: 2000000 INFO @ Tue, 14 Jul 2020 11:10:10: 3000000 INFO @ Tue, 14 Jul 2020 11:10:16: 4000000 INFO @ Tue, 14 Jul 2020 11:10:17: #1 tag size is determined as 66 bps INFO @ Tue, 14 Jul 2020 11:10:17: #1 tag size = 66 INFO @ Tue, 14 Jul 2020 11:10:17: #1 total tags in treatment: 4137867 INFO @ Tue, 14 Jul 2020 11:10:17: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:10:17: #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 11:10:17: #1 tags after filtering in treatment: 4137867 INFO @ Tue, 14 Jul 2020 11:10:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:10:17: #1 finished! INFO @ Tue, 14 Jul 2020 11:10:17: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:10:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:10:17: #2 number of paired peaks: 562 WARNING @ Tue, 14 Jul 2020 11:10:17: Fewer paired peaks (562) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 562 pairs to build model! INFO @ Tue, 14 Jul 2020 11:10:17: start model_add_line... INFO @ Tue, 14 Jul 2020 11:10:17: start X-correlation... INFO @ Tue, 14 Jul 2020 11:10:17: end of X-cor INFO @ Tue, 14 Jul 2020 11:10:17: #2 finished! INFO @ Tue, 14 Jul 2020 11:10:17: #2 predicted fragment length is 63 bps INFO @ Tue, 14 Jul 2020 11:10:17: #2 alternative fragment length(s) may be 63,514,518 bps INFO @ Tue, 14 Jul 2020 11:10:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521348/SRX8521348.05_model.r WARNING @ Tue, 14 Jul 2020 11:10:17: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:10:17: #2 You may need to consider one of the other alternative d(s): 63,514,518 WARNING @ Tue, 14 Jul 2020 11:10:17: #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 11:10:17: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:10:17: #3 Pre-compute pvalue-qvalue table... 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 11:10:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521348/SRX8521348.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521348/SRX8521348.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521348/SRX8521348.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521348/SRX8521348.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 11:10:24: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:10:24: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:10:26: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:10:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521348/SRX8521348.05_peaks.xls INFO @ Tue, 14 Jul 2020 11:10:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521348/SRX8521348.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:10:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521348/SRX8521348.05_summits.bed INFO @ Tue, 14 Jul 2020 11:10:31: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1829 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:10:32: 1000000 INFO @ Tue, 14 Jul 2020 11:10:41: 2000000 INFO @ Tue, 14 Jul 2020 11:10:50: 3000000 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 11:10:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521348/SRX8521348.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521348/SRX8521348.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521348/SRX8521348.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521348/SRX8521348.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 11:10:53: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:10:53: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:10:59: 4000000 INFO @ Tue, 14 Jul 2020 11:11:00: #1 tag size is determined as 66 bps INFO @ Tue, 14 Jul 2020 11:11:00: #1 tag size = 66 INFO @ Tue, 14 Jul 2020 11:11:00: #1 total tags in treatment: 4137867 INFO @ Tue, 14 Jul 2020 11:11:00: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:11:00: #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 11:11:00: #1 tags after filtering in treatment: 4137867 INFO @ Tue, 14 Jul 2020 11:11:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:11:00: #1 finished! INFO @ Tue, 14 Jul 2020 11:11:00: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:11:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:11:01: 1000000 INFO @ Tue, 14 Jul 2020 11:11:01: #2 number of paired peaks: 562 WARNING @ Tue, 14 Jul 2020 11:11:01: Fewer paired peaks (562) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 562 pairs to build model! INFO @ Tue, 14 Jul 2020 11:11:01: start model_add_line... INFO @ Tue, 14 Jul 2020 11:11:01: start X-correlation... INFO @ Tue, 14 Jul 2020 11:11:01: end of X-cor INFO @ Tue, 14 Jul 2020 11:11:01: #2 finished! INFO @ Tue, 14 Jul 2020 11:11:01: #2 predicted fragment length is 63 bps INFO @ Tue, 14 Jul 2020 11:11:01: #2 alternative fragment length(s) may be 63,514,518 bps INFO @ Tue, 14 Jul 2020 11:11:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521348/SRX8521348.10_model.r WARNING @ Tue, 14 Jul 2020 11:11:01: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:11:01: #2 You may need to consider one of the other alternative d(s): 63,514,518 WARNING @ Tue, 14 Jul 2020 11:11:01: #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 11:11:01: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:11:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:11:07: 2000000 INFO @ Tue, 14 Jul 2020 11:11:10: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:11:14: 3000000 INFO @ Tue, 14 Jul 2020 11:11:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521348/SRX8521348.10_peaks.xls INFO @ Tue, 14 Jul 2020 11:11:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521348/SRX8521348.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:11:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521348/SRX8521348.10_summits.bed INFO @ Tue, 14 Jul 2020 11:11:15: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (649 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 11:11:21: 4000000 INFO @ Tue, 14 Jul 2020 11:11:22: #1 tag size is determined as 66 bps INFO @ Tue, 14 Jul 2020 11:11:22: #1 tag size = 66 INFO @ Tue, 14 Jul 2020 11:11:22: #1 total tags in treatment: 4137867 INFO @ Tue, 14 Jul 2020 11:11:22: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:11:22: #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 11:11:22: #1 tags after filtering in treatment: 4137867 INFO @ Tue, 14 Jul 2020 11:11:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:11:22: #1 finished! INFO @ Tue, 14 Jul 2020 11:11:22: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:11:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:11:22: #2 number of paired peaks: 562 WARNING @ Tue, 14 Jul 2020 11:11:22: Fewer paired peaks (562) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 562 pairs to build model! INFO @ Tue, 14 Jul 2020 11:11:22: start model_add_line... INFO @ Tue, 14 Jul 2020 11:11:22: start X-correlation... INFO @ Tue, 14 Jul 2020 11:11:22: end of X-cor INFO @ Tue, 14 Jul 2020 11:11:22: #2 finished! INFO @ Tue, 14 Jul 2020 11:11:22: #2 predicted fragment length is 63 bps INFO @ Tue, 14 Jul 2020 11:11:22: #2 alternative fragment length(s) may be 63,514,518 bps INFO @ Tue, 14 Jul 2020 11:11:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521348/SRX8521348.20_model.r WARNING @ Tue, 14 Jul 2020 11:11:22: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:11:22: #2 You may need to consider one of the other alternative d(s): 63,514,518 WARNING @ Tue, 14 Jul 2020 11:11:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 11:11:22: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:11:22: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 11:11:32: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:11:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521348/SRX8521348.20_peaks.xls INFO @ Tue, 14 Jul 2020 11:11:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521348/SRX8521348.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:11:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521348/SRX8521348.20_summits.bed INFO @ Tue, 14 Jul 2020 11:11:36: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (148 records, 4 fields): 1 millis CompletedMACS2peakCalling