Job ID = 6627311 SRX = SRX8521367 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T01:57:09 prefetch.2.10.7: 1) Downloading 'SRR11978134'... 2020-07-14T01:57:09 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:58:57 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:58:58 prefetch.2.10.7: 'SRR11978134' is valid 2020-07-14T01:58:58 prefetch.2.10.7: 1) 'SRR11978134' was downloaded successfully 2020-07-14T01:58:58 prefetch.2.10.7: 'SRR11978134' has 0 unresolved dependencies Read 12167233 spots for SRR11978134/SRR11978134.sra Written 12167233 spots for SRR11978134/SRR11978134.sra 2020-07-14T01:59:51 prefetch.2.10.7: 1) Downloading 'SRR11978135'... 2020-07-14T01:59:51 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:01:16 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:01:17 prefetch.2.10.7: 'SRR11978135' is valid 2020-07-14T02:01:17 prefetch.2.10.7: 1) 'SRR11978135' was downloaded successfully 2020-07-14T02:01:17 prefetch.2.10.7: 'SRR11978135' has 0 unresolved dependencies Read 11127472 spots for SRR11978135/SRR11978135.sra Written 11127472 spots for SRR11978135/SRR11978135.sra 2020-07-14T02:02:08 prefetch.2.10.7: 1) Downloading 'SRR11978136'... 2020-07-14T02:02:08 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:03:57 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:03:57 prefetch.2.10.7: 'SRR11978136' is valid 2020-07-14T02:03:57 prefetch.2.10.7: 1) 'SRR11978136' was downloaded successfully 2020-07-14T02:03:57 prefetch.2.10.7: 'SRR11978136' has 0 unresolved dependencies Read 11630832 spots for SRR11978136/SRR11978136.sra Written 11630832 spots for SRR11978136/SRR11978136.sra 2020-07-14T02:04:51 prefetch.2.10.7: 1) Downloading 'SRR11978137'... 2020-07-14T02:04:51 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:05:49 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:05:49 prefetch.2.10.7: 'SRR11978137' is valid 2020-07-14T02:05:49 prefetch.2.10.7: 1) 'SRR11978137' was downloaded successfully 2020-07-14T02:05:49 prefetch.2.10.7: 'SRR11978137' has 0 unresolved dependencies Read 11712096 spots for SRR11978137/SRR11978137.sra Written 11712096 spots for SRR11978137/SRR11978137.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627547 ("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: 00:08:53 46637633 reads; of these: 46637633 (100.00%) were unpaired; of these: 35698821 (76.55%) aligned 0 times 7375408 (15.81%) aligned exactly 1 time 3563404 (7.64%) aligned >1 times 23.45% overall alignment rate Time searching: 00:08:53 Overall time: 00:08:53 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 8 files... [bam_rmdupse_core] 2371520 / 10938812 = 0.2168 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 11:19:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521367/SRX8521367.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521367/SRX8521367.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521367/SRX8521367.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521367/SRX8521367.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 11:19:08: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:19:08: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:19:16: 1000000 INFO @ Tue, 14 Jul 2020 11:19:24: 2000000 INFO @ Tue, 14 Jul 2020 11:19:32: 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 11:19:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521367/SRX8521367.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521367/SRX8521367.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521367/SRX8521367.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521367/SRX8521367.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 11:19:38: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:19:38: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:19:40: 4000000 INFO @ Tue, 14 Jul 2020 11:19:47: 1000000 INFO @ Tue, 14 Jul 2020 11:19:48: 5000000 INFO @ Tue, 14 Jul 2020 11:19:55: 2000000 INFO @ Tue, 14 Jul 2020 11:19:57: 6000000 INFO @ Tue, 14 Jul 2020 11:20:03: 3000000 INFO @ Tue, 14 Jul 2020 11:20:05: 7000000 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 11:20:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521367/SRX8521367.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521367/SRX8521367.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521367/SRX8521367.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521367/SRX8521367.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 11:20:08: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:20:08: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:20:12: 4000000 INFO @ Tue, 14 Jul 2020 11:20:13: 8000000 INFO @ Tue, 14 Jul 2020 11:20:17: 1000000 INFO @ Tue, 14 Jul 2020 11:20:18: #1 tag size is determined as 68 bps INFO @ Tue, 14 Jul 2020 11:20:18: #1 tag size = 68 INFO @ Tue, 14 Jul 2020 11:20:18: #1 total tags in treatment: 8567292 INFO @ Tue, 14 Jul 2020 11:20:18: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:20:18: #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 11:20:18: #1 tags after filtering in treatment: 8567292 INFO @ Tue, 14 Jul 2020 11:20:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:20:18: #1 finished! INFO @ Tue, 14 Jul 2020 11:20:18: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:20:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:20:19: #2 number of paired peaks: 159 WARNING @ Tue, 14 Jul 2020 11:20:19: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Tue, 14 Jul 2020 11:20:19: start model_add_line... INFO @ Tue, 14 Jul 2020 11:20:19: start X-correlation... INFO @ Tue, 14 Jul 2020 11:20:19: end of X-cor INFO @ Tue, 14 Jul 2020 11:20:19: #2 finished! INFO @ Tue, 14 Jul 2020 11:20:19: #2 predicted fragment length is 66 bps INFO @ Tue, 14 Jul 2020 11:20:19: #2 alternative fragment length(s) may be 66 bps INFO @ Tue, 14 Jul 2020 11:20:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521367/SRX8521367.05_model.r WARNING @ Tue, 14 Jul 2020 11:20:19: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:20:19: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Tue, 14 Jul 2020 11:20:19: #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 11:20:19: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:20:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:20:20: 5000000 INFO @ Tue, 14 Jul 2020 11:20:26: 2000000 INFO @ Tue, 14 Jul 2020 11:20:29: 6000000 INFO @ Tue, 14 Jul 2020 11:20:34: 3000000 INFO @ Tue, 14 Jul 2020 11:20:36: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:20:37: 7000000 INFO @ Tue, 14 Jul 2020 11:20:43: 4000000 INFO @ Tue, 14 Jul 2020 11:20:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521367/SRX8521367.05_peaks.xls INFO @ Tue, 14 Jul 2020 11:20:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521367/SRX8521367.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:20:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521367/SRX8521367.05_summits.bed INFO @ Tue, 14 Jul 2020 11:20:45: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1917 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:20:46: 8000000 INFO @ Tue, 14 Jul 2020 11:20:51: #1 tag size is determined as 68 bps INFO @ Tue, 14 Jul 2020 11:20:51: #1 tag size = 68 INFO @ Tue, 14 Jul 2020 11:20:51: #1 total tags in treatment: 8567292 INFO @ Tue, 14 Jul 2020 11:20:51: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:20:51: #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 11:20:51: #1 tags after filtering in treatment: 8567292 INFO @ Tue, 14 Jul 2020 11:20:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:20:51: #1 finished! INFO @ Tue, 14 Jul 2020 11:20:51: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:20:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:20:51: #2 number of paired peaks: 159 WARNING @ Tue, 14 Jul 2020 11:20:51: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Tue, 14 Jul 2020 11:20:51: start model_add_line... INFO @ Tue, 14 Jul 2020 11:20:51: 5000000 INFO @ Tue, 14 Jul 2020 11:20:52: start X-correlation... INFO @ Tue, 14 Jul 2020 11:20:52: end of X-cor INFO @ Tue, 14 Jul 2020 11:20:52: #2 finished! INFO @ Tue, 14 Jul 2020 11:20:52: #2 predicted fragment length is 66 bps INFO @ Tue, 14 Jul 2020 11:20:52: #2 alternative fragment length(s) may be 66 bps INFO @ Tue, 14 Jul 2020 11:20:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521367/SRX8521367.10_model.r WARNING @ Tue, 14 Jul 2020 11:20:52: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:20:52: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Tue, 14 Jul 2020 11:20:52: #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 11:20:52: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:20:52: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 11:20:59: 6000000 INFO @ Tue, 14 Jul 2020 11:21:07: 7000000 INFO @ Tue, 14 Jul 2020 11:21:09: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 11:21:15: 8000000 INFO @ Tue, 14 Jul 2020 11:21:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521367/SRX8521367.10_peaks.xls INFO @ Tue, 14 Jul 2020 11:21:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521367/SRX8521367.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:21:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521367/SRX8521367.10_summits.bed INFO @ Tue, 14 Jul 2020 11:21:18: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1003 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:21:19: #1 tag size is determined as 68 bps INFO @ Tue, 14 Jul 2020 11:21:19: #1 tag size = 68 INFO @ Tue, 14 Jul 2020 11:21:19: #1 total tags in treatment: 8567292 INFO @ Tue, 14 Jul 2020 11:21:19: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:21:19: #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 11:21:19: #1 tags after filtering in treatment: 8567292 INFO @ Tue, 14 Jul 2020 11:21:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:21:19: #1 finished! INFO @ Tue, 14 Jul 2020 11:21:19: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:21:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:21:20: #2 number of paired peaks: 159 WARNING @ Tue, 14 Jul 2020 11:21:20: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Tue, 14 Jul 2020 11:21:20: start model_add_line... INFO @ Tue, 14 Jul 2020 11:21:20: start X-correlation... INFO @ Tue, 14 Jul 2020 11:21:20: end of X-cor INFO @ Tue, 14 Jul 2020 11:21:20: #2 finished! INFO @ Tue, 14 Jul 2020 11:21:20: #2 predicted fragment length is 66 bps INFO @ Tue, 14 Jul 2020 11:21:20: #2 alternative fragment length(s) may be 66 bps INFO @ Tue, 14 Jul 2020 11:21:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521367/SRX8521367.20_model.r WARNING @ Tue, 14 Jul 2020 11:21:20: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:21:20: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Tue, 14 Jul 2020 11:21:20: #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 11:21:20: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:21:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:21:38: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:21:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521367/SRX8521367.20_peaks.xls INFO @ Tue, 14 Jul 2020 11:21:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521367/SRX8521367.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:21:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521367/SRX8521367.20_summits.bed INFO @ Tue, 14 Jul 2020 11:21:47: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (348 records, 4 fields): 2 millis CompletedMACS2peakCalling