Job ID = 6627503 SRX = SRX8521396 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T02:45:03 prefetch.2.10.7: 1) Downloading 'SRR11978326'... 2020-07-14T02:45:03 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:45:56 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:45:56 prefetch.2.10.7: 'SRR11978326' is valid 2020-07-14T02:45:56 prefetch.2.10.7: 1) 'SRR11978326' was downloaded successfully 2020-07-14T02:45:56 prefetch.2.10.7: 'SRR11978326' has 0 unresolved dependencies Read 12199549 spots for SRR11978326/SRR11978326.sra Written 12199549 spots for SRR11978326/SRR11978326.sra 2020-07-14T02:46:52 prefetch.2.10.7: 1) Downloading 'SRR11978327'... 2020-07-14T02:46:52 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:47:53 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:47:53 prefetch.2.10.7: 'SRR11978327' is valid 2020-07-14T02:47:53 prefetch.2.10.7: 1) 'SRR11978327' was downloaded successfully 2020-07-14T02:47:53 prefetch.2.10.7: 'SRR11978327' has 0 unresolved dependencies Read 12154346 spots for SRR11978327/SRR11978327.sra Written 12154346 spots for SRR11978327/SRR11978327.sra 2020-07-14T02:48:48 prefetch.2.10.7: 1) Downloading 'SRR11978328'... 2020-07-14T02:48:48 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:50:18 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:50:19 prefetch.2.10.7: 'SRR11978328' is valid 2020-07-14T02:50:19 prefetch.2.10.7: 1) 'SRR11978328' was downloaded successfully 2020-07-14T02:50:19 prefetch.2.10.7: 'SRR11978328' has 0 unresolved dependencies Read 12023816 spots for SRR11978328/SRR11978328.sra Written 12023816 spots for SRR11978328/SRR11978328.sra 2020-07-14T02:51:12 prefetch.2.10.7: 1) Downloading 'SRR11978329'... 2020-07-14T02:51:12 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:53:09 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:53:09 prefetch.2.10.7: 'SRR11978329' is valid 2020-07-14T02:53:09 prefetch.2.10.7: 1) 'SRR11978329' was downloaded successfully 2020-07-14T02:53:09 prefetch.2.10.7: 'SRR11978329' has 0 unresolved dependencies Read 12134049 spots for SRR11978329/SRR11978329.sra Written 12134049 spots for SRR11978329/SRR11978329.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627697 ("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: 00:08:48 48511760 reads; of these: 48511760 (100.00%) were unpaired; of these: 38551984 (79.47%) aligned 0 times 6888669 (14.20%) aligned exactly 1 time 3071107 (6.33%) aligned >1 times 20.53% overall alignment rate Time searching: 00:08:48 Overall time: 00:08:48 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] 1752327 / 9959776 = 0.1759 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 12:06:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521396/SRX8521396.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521396/SRX8521396.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521396/SRX8521396.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521396/SRX8521396.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 12:06:02: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:06:02: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:06:08: 1000000 INFO @ Tue, 14 Jul 2020 12:06:13: 2000000 INFO @ Tue, 14 Jul 2020 12:06:19: 3000000 INFO @ Tue, 14 Jul 2020 12:06:24: 4000000 INFO @ Tue, 14 Jul 2020 12:06:30: 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, 14 Jul 2020 12:06:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521396/SRX8521396.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521396/SRX8521396.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521396/SRX8521396.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521396/SRX8521396.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 12:06:32: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:06:32: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:06:36: 6000000 INFO @ Tue, 14 Jul 2020 12:06:40: 1000000 INFO @ Tue, 14 Jul 2020 12:06:42: 7000000 INFO @ Tue, 14 Jul 2020 12:06:47: 2000000 INFO @ Tue, 14 Jul 2020 12:06:49: 8000000 INFO @ Tue, 14 Jul 2020 12:06:50: #1 tag size is determined as 63 bps INFO @ Tue, 14 Jul 2020 12:06:50: #1 tag size = 63 INFO @ Tue, 14 Jul 2020 12:06:50: #1 total tags in treatment: 8207449 INFO @ Tue, 14 Jul 2020 12:06:50: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:06:50: #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 12:06:50: #1 tags after filtering in treatment: 8207449 INFO @ Tue, 14 Jul 2020 12:06:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:06:50: #1 finished! INFO @ Tue, 14 Jul 2020 12:06:50: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:06:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:06:51: #2 number of paired peaks: 180 WARNING @ Tue, 14 Jul 2020 12:06:51: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Tue, 14 Jul 2020 12:06:51: start model_add_line... INFO @ Tue, 14 Jul 2020 12:06:51: start X-correlation... INFO @ Tue, 14 Jul 2020 12:06:51: end of X-cor INFO @ Tue, 14 Jul 2020 12:06:51: #2 finished! INFO @ Tue, 14 Jul 2020 12:06:51: #2 predicted fragment length is 54 bps INFO @ Tue, 14 Jul 2020 12:06:51: #2 alternative fragment length(s) may be 54 bps INFO @ Tue, 14 Jul 2020 12:06:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521396/SRX8521396.05_model.r WARNING @ Tue, 14 Jul 2020 12:06:51: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:06:51: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Tue, 14 Jul 2020 12:06:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 12:06:51: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:06:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:06:54: 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 12:07:01: 4000000 INFO @ Tue, 14 Jul 2020 12:07:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521396/SRX8521396.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521396/SRX8521396.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521396/SRX8521396.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521396/SRX8521396.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 12:07:02: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:07:02: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:07:07: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:07:08: 5000000 INFO @ Tue, 14 Jul 2020 12:07:09: 1000000 INFO @ Tue, 14 Jul 2020 12:07:15: 6000000 INFO @ Tue, 14 Jul 2020 12:07:15: 2000000 INFO @ Tue, 14 Jul 2020 12:07:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521396/SRX8521396.05_peaks.xls INFO @ Tue, 14 Jul 2020 12:07:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521396/SRX8521396.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:07:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521396/SRX8521396.05_summits.bed INFO @ Tue, 14 Jul 2020 12:07:15: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1527 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 12:07:22: 3000000 INFO @ Tue, 14 Jul 2020 12:07:22: 7000000 INFO @ Tue, 14 Jul 2020 12:07:28: 4000000 INFO @ Tue, 14 Jul 2020 12:07:30: 8000000 INFO @ Tue, 14 Jul 2020 12:07:31: #1 tag size is determined as 63 bps INFO @ Tue, 14 Jul 2020 12:07:31: #1 tag size = 63 INFO @ Tue, 14 Jul 2020 12:07:31: #1 total tags in treatment: 8207449 INFO @ Tue, 14 Jul 2020 12:07:31: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:07:31: #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 12:07:31: #1 tags after filtering in treatment: 8207449 INFO @ Tue, 14 Jul 2020 12:07:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:07:31: #1 finished! INFO @ Tue, 14 Jul 2020 12:07:31: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:07:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:07:32: #2 number of paired peaks: 180 WARNING @ Tue, 14 Jul 2020 12:07:32: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Tue, 14 Jul 2020 12:07:32: start model_add_line... INFO @ Tue, 14 Jul 2020 12:07:32: start X-correlation... INFO @ Tue, 14 Jul 2020 12:07:32: end of X-cor INFO @ Tue, 14 Jul 2020 12:07:32: #2 finished! INFO @ Tue, 14 Jul 2020 12:07:32: #2 predicted fragment length is 54 bps INFO @ Tue, 14 Jul 2020 12:07:32: #2 alternative fragment length(s) may be 54 bps INFO @ Tue, 14 Jul 2020 12:07:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521396/SRX8521396.10_model.r WARNING @ Tue, 14 Jul 2020 12:07:32: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:07:32: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Tue, 14 Jul 2020 12:07:32: #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 12:07:32: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:07:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:07:34: 5000000 INFO @ Tue, 14 Jul 2020 12:07:40: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 12:07:46: 7000000 INFO @ Tue, 14 Jul 2020 12:07:49: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:07:52: 8000000 INFO @ Tue, 14 Jul 2020 12:07:53: #1 tag size is determined as 63 bps INFO @ Tue, 14 Jul 2020 12:07:53: #1 tag size = 63 INFO @ Tue, 14 Jul 2020 12:07:53: #1 total tags in treatment: 8207449 INFO @ Tue, 14 Jul 2020 12:07:53: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:07:53: #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 12:07:53: #1 tags after filtering in treatment: 8207449 INFO @ Tue, 14 Jul 2020 12:07:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:07:53: #1 finished! INFO @ Tue, 14 Jul 2020 12:07:53: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:07:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:07:54: #2 number of paired peaks: 180 WARNING @ Tue, 14 Jul 2020 12:07:54: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Tue, 14 Jul 2020 12:07:54: start model_add_line... INFO @ Tue, 14 Jul 2020 12:07:54: start X-correlation... INFO @ Tue, 14 Jul 2020 12:07:54: end of X-cor INFO @ Tue, 14 Jul 2020 12:07:54: #2 finished! INFO @ Tue, 14 Jul 2020 12:07:54: #2 predicted fragment length is 54 bps INFO @ Tue, 14 Jul 2020 12:07:54: #2 alternative fragment length(s) may be 54 bps INFO @ Tue, 14 Jul 2020 12:07:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521396/SRX8521396.20_model.r WARNING @ Tue, 14 Jul 2020 12:07:54: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:07:54: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Tue, 14 Jul 2020 12:07:54: #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 12:07:54: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:07:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:07:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521396/SRX8521396.10_peaks.xls INFO @ Tue, 14 Jul 2020 12:07:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521396/SRX8521396.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:07:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521396/SRX8521396.10_summits.bed INFO @ Tue, 14 Jul 2020 12:07:57: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (750 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 12:08:10: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:08:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521396/SRX8521396.20_peaks.xls INFO @ Tue, 14 Jul 2020 12:08:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521396/SRX8521396.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:08:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521396/SRX8521396.20_summits.bed INFO @ Tue, 14 Jul 2020 12:08:18: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (341 records, 4 fields): 1 millis CompletedMACS2peakCalling