Job ID = 6627319 SRX = SRX8521368 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T01:57:51 prefetch.2.10.7: 1) Downloading 'SRR11978138'... 2020-07-14T01:57:51 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:59:27 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:59:28 prefetch.2.10.7: 'SRR11978138' is valid 2020-07-14T01:59:28 prefetch.2.10.7: 1) 'SRR11978138' was downloaded successfully 2020-07-14T01:59:28 prefetch.2.10.7: 'SRR11978138' has 0 unresolved dependencies Read 12618274 spots for SRR11978138/SRR11978138.sra Written 12618274 spots for SRR11978138/SRR11978138.sra 2020-07-14T02:00:20 prefetch.2.10.7: 1) Downloading 'SRR11978139'... 2020-07-14T02:00:20 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:01:33 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:01:34 prefetch.2.10.7: 'SRR11978139' is valid 2020-07-14T02:01:34 prefetch.2.10.7: 1) 'SRR11978139' was downloaded successfully 2020-07-14T02:01:34 prefetch.2.10.7: 'SRR11978139' has 0 unresolved dependencies Read 11570747 spots for SRR11978139/SRR11978139.sra Written 11570747 spots for SRR11978139/SRR11978139.sra 2020-07-14T02:02:22 prefetch.2.10.7: 1) Downloading 'SRR11978140'... 2020-07-14T02:02:22 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:03:34 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:03:34 prefetch.2.10.7: 'SRR11978140' is valid 2020-07-14T02:03:34 prefetch.2.10.7: 1) 'SRR11978140' was downloaded successfully 2020-07-14T02:03:34 prefetch.2.10.7: 'SRR11978140' has 0 unresolved dependencies Read 12054853 spots for SRR11978140/SRR11978140.sra Written 12054853 spots for SRR11978140/SRR11978140.sra 2020-07-14T02:04:27 prefetch.2.10.7: 1) Downloading 'SRR11978141'... 2020-07-14T02:04:27 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:05:40 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:05:40 prefetch.2.10.7: 'SRR11978141' is valid 2020-07-14T02:05:40 prefetch.2.10.7: 1) 'SRR11978141' was downloaded successfully 2020-07-14T02:05:40 prefetch.2.10.7: 'SRR11978141' has 0 unresolved dependencies Read 12142215 spots for SRR11978141/SRR11978141.sra Written 12142215 spots for SRR11978141/SRR11978141.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627536 ("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: 00:07:02 48386089 reads; of these: 48386089 (100.00%) were unpaired; of these: 41415938 (85.59%) aligned 0 times 5115981 (10.57%) aligned exactly 1 time 1854170 (3.83%) aligned >1 times 14.41% overall alignment rate Time searching: 00:07:02 Overall time: 00:07:02 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] 1287255 / 6970151 = 0.1847 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 11:16:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521368/SRX8521368.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521368/SRX8521368.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521368/SRX8521368.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521368/SRX8521368.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 11:16:08: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:16:08: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:16:15: 1000000 INFO @ Tue, 14 Jul 2020 11:16:22: 2000000 INFO @ Tue, 14 Jul 2020 11:16:29: 3000000 INFO @ Tue, 14 Jul 2020 11:16:35: 4000000 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 11:16:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521368/SRX8521368.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521368/SRX8521368.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521368/SRX8521368.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521368/SRX8521368.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 11:16:38: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:16:38: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:16:42: 5000000 INFO @ Tue, 14 Jul 2020 11:16:45: 1000000 INFO @ Tue, 14 Jul 2020 11:16:47: #1 tag size is determined as 62 bps INFO @ Tue, 14 Jul 2020 11:16:47: #1 tag size = 62 INFO @ Tue, 14 Jul 2020 11:16:47: #1 total tags in treatment: 5682896 INFO @ Tue, 14 Jul 2020 11:16:47: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:16:47: #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 11:16:47: #1 tags after filtering in treatment: 5682896 INFO @ Tue, 14 Jul 2020 11:16:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:16:47: #1 finished! INFO @ Tue, 14 Jul 2020 11:16:47: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:16:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:16:47: #2 number of paired peaks: 348 WARNING @ Tue, 14 Jul 2020 11:16:47: Fewer paired peaks (348) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 348 pairs to build model! INFO @ Tue, 14 Jul 2020 11:16:47: start model_add_line... INFO @ Tue, 14 Jul 2020 11:16:47: start X-correlation... INFO @ Tue, 14 Jul 2020 11:16:47: end of X-cor INFO @ Tue, 14 Jul 2020 11:16:47: #2 finished! INFO @ Tue, 14 Jul 2020 11:16:47: #2 predicted fragment length is 58 bps INFO @ Tue, 14 Jul 2020 11:16:47: #2 alternative fragment length(s) may be 58,532 bps INFO @ Tue, 14 Jul 2020 11:16:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521368/SRX8521368.05_model.r WARNING @ Tue, 14 Jul 2020 11:16:47: #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 11:16:47: #2 You may need to consider one of the other alternative d(s): 58,532 WARNING @ Tue, 14 Jul 2020 11:16:47: #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 11:16:47: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:16:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:16:52: 2000000 INFO @ Tue, 14 Jul 2020 11:16:59: 3000000 INFO @ Tue, 14 Jul 2020 11:16:59: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:17:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521368/SRX8521368.05_peaks.xls INFO @ Tue, 14 Jul 2020 11:17:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521368/SRX8521368.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:17:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521368/SRX8521368.05_summits.bed INFO @ Tue, 14 Jul 2020 11:17:06: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1776 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:17:06: 4000000 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 11:17:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521368/SRX8521368.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521368/SRX8521368.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521368/SRX8521368.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521368/SRX8521368.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 11:17:08: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:17:08: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:17:13: 5000000 INFO @ Tue, 14 Jul 2020 11:17:16: 1000000 INFO @ Tue, 14 Jul 2020 11:17:18: #1 tag size is determined as 62 bps INFO @ Tue, 14 Jul 2020 11:17:18: #1 tag size = 62 INFO @ Tue, 14 Jul 2020 11:17:18: #1 total tags in treatment: 5682896 INFO @ Tue, 14 Jul 2020 11:17:18: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:17:18: #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 11:17:18: #1 tags after filtering in treatment: 5682896 INFO @ Tue, 14 Jul 2020 11:17:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:17:18: #1 finished! INFO @ Tue, 14 Jul 2020 11:17:18: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:17:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:17:19: #2 number of paired peaks: 348 WARNING @ Tue, 14 Jul 2020 11:17:19: Fewer paired peaks (348) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 348 pairs to build model! INFO @ Tue, 14 Jul 2020 11:17:19: start model_add_line... INFO @ Tue, 14 Jul 2020 11:17:19: start X-correlation... INFO @ Tue, 14 Jul 2020 11:17:19: end of X-cor INFO @ Tue, 14 Jul 2020 11:17:19: #2 finished! INFO @ Tue, 14 Jul 2020 11:17:19: #2 predicted fragment length is 58 bps INFO @ Tue, 14 Jul 2020 11:17:19: #2 alternative fragment length(s) may be 58,532 bps INFO @ Tue, 14 Jul 2020 11:17:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521368/SRX8521368.10_model.r WARNING @ Tue, 14 Jul 2020 11:17:19: #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 11:17:19: #2 You may need to consider one of the other alternative d(s): 58,532 WARNING @ Tue, 14 Jul 2020 11:17:19: #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 11:17:19: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:17:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:17:23: 2000000 INFO @ Tue, 14 Jul 2020 11:17:30: 3000000 INFO @ Tue, 14 Jul 2020 11:17:30: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 11:17:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521368/SRX8521368.10_peaks.xls INFO @ Tue, 14 Jul 2020 11:17:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521368/SRX8521368.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:17:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521368/SRX8521368.10_summits.bed INFO @ Tue, 14 Jul 2020 11:17:36: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (746 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:17:36: 4000000 INFO @ Tue, 14 Jul 2020 11:17:43: 5000000 INFO @ Tue, 14 Jul 2020 11:17:48: #1 tag size is determined as 62 bps INFO @ Tue, 14 Jul 2020 11:17:48: #1 tag size = 62 INFO @ Tue, 14 Jul 2020 11:17:48: #1 total tags in treatment: 5682896 INFO @ Tue, 14 Jul 2020 11:17:48: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:17:48: #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 11:17:48: #1 tags after filtering in treatment: 5682896 INFO @ Tue, 14 Jul 2020 11:17:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:17:48: #1 finished! INFO @ Tue, 14 Jul 2020 11:17:48: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:17:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:17:48: #2 number of paired peaks: 348 WARNING @ Tue, 14 Jul 2020 11:17:48: Fewer paired peaks (348) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 348 pairs to build model! INFO @ Tue, 14 Jul 2020 11:17:48: start model_add_line... INFO @ Tue, 14 Jul 2020 11:17:49: start X-correlation... INFO @ Tue, 14 Jul 2020 11:17:49: end of X-cor INFO @ Tue, 14 Jul 2020 11:17:49: #2 finished! INFO @ Tue, 14 Jul 2020 11:17:49: #2 predicted fragment length is 58 bps INFO @ Tue, 14 Jul 2020 11:17:49: #2 alternative fragment length(s) may be 58,532 bps INFO @ Tue, 14 Jul 2020 11:17:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521368/SRX8521368.20_model.r WARNING @ Tue, 14 Jul 2020 11:17:49: #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 11:17:49: #2 You may need to consider one of the other alternative d(s): 58,532 WARNING @ Tue, 14 Jul 2020 11:17:49: #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 11:17:49: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:17:49: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 11:18:00: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:18:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521368/SRX8521368.20_peaks.xls INFO @ Tue, 14 Jul 2020 11:18:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521368/SRX8521368.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:18:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521368/SRX8521368.20_summits.bed INFO @ Tue, 14 Jul 2020 11:18:06: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (146 records, 4 fields): 1 millis CompletedMACS2peakCalling