Job ID = 6627265 SRX = SRX8521334 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T01:42:50 prefetch.2.10.7: 1) Downloading 'SRR11978029'... 2020-07-14T01:42:50 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:43:43 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:43:44 prefetch.2.10.7: 'SRR11978029' is valid 2020-07-14T01:43:44 prefetch.2.10.7: 1) 'SRR11978029' was downloaded successfully 2020-07-14T01:43:44 prefetch.2.10.7: 'SRR11978029' has 0 unresolved dependencies Read 5625009 spots for SRR11978029/SRR11978029.sra Written 5625009 spots for SRR11978029/SRR11978029.sra 2020-07-14T01:44:14 prefetch.2.10.7: 1) Downloading 'SRR11978030'... 2020-07-14T01:44:14 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:44:59 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:44:59 prefetch.2.10.7: 'SRR11978030' is valid 2020-07-14T01:44:59 prefetch.2.10.7: 1) 'SRR11978030' was downloaded successfully 2020-07-14T01:44:59 prefetch.2.10.7: 'SRR11978030' has 0 unresolved dependencies Read 5329445 spots for SRR11978030/SRR11978030.sra Written 5329445 spots for SRR11978030/SRR11978030.sra 2020-07-14T01:45:28 prefetch.2.10.7: 1) Downloading 'SRR11978031'... 2020-07-14T01:45:28 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:46:15 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:46:15 prefetch.2.10.7: 'SRR11978031' is valid 2020-07-14T01:46:15 prefetch.2.10.7: 1) 'SRR11978031' was downloaded successfully 2020-07-14T01:46:15 prefetch.2.10.7: 'SRR11978031' has 0 unresolved dependencies Read 5848302 spots for SRR11978031/SRR11978031.sra Written 5848302 spots for SRR11978031/SRR11978031.sra 2020-07-14T01:46:49 prefetch.2.10.7: 1) Downloading 'SRR11978032'... 2020-07-14T01:46:49 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:48:09 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:48:09 prefetch.2.10.7: 'SRR11978032' is valid 2020-07-14T01:48:09 prefetch.2.10.7: 1) 'SRR11978032' was downloaded successfully 2020-07-14T01:48:09 prefetch.2.10.7: 'SRR11978032' has 0 unresolved dependencies Read 5885207 spots for SRR11978032/SRR11978032.sra Written 5885207 spots for SRR11978032/SRR11978032.sra 2020-07-14T01:48:40 prefetch.2.10.7: 1) Downloading 'SRR11978033'... 2020-07-14T01:48:40 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:51:31 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:51:32 prefetch.2.10.7: 'SRR11978033' is valid 2020-07-14T01:51:32 prefetch.2.10.7: 1) 'SRR11978033' was downloaded successfully 2020-07-14T01:51:32 prefetch.2.10.7: 'SRR11978033' has 0 unresolved dependencies Read 9502935 spots for SRR11978033/SRR11978033.sra Written 9502935 spots for SRR11978033/SRR11978033.sra 2020-07-14T01:52:19 prefetch.2.10.7: 1) Downloading 'SRR11978034'... 2020-07-14T01:52:19 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:53:49 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:53:49 prefetch.2.10.7: 'SRR11978034' is valid 2020-07-14T01:53:49 prefetch.2.10.7: 1) 'SRR11978034' was downloaded successfully 2020-07-14T01:53:49 prefetch.2.10.7: 'SRR11978034' has 0 unresolved dependencies Read 9176959 spots for SRR11978034/SRR11978034.sra Written 9176959 spots for SRR11978034/SRR11978034.sra 2020-07-14T01:54:31 prefetch.2.10.7: 1) Downloading 'SRR11978035'... 2020-07-14T01:54:31 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: 'SRR11978035' is valid 2020-07-14T01:55:51 prefetch.2.10.7: 1) 'SRR11978035' was downloaded successfully 2020-07-14T01:55:51 prefetch.2.10.7: 'SRR11978035' has 0 unresolved dependencies Read 9766531 spots for SRR11978035/SRR11978035.sra Written 9766531 spots for SRR11978035/SRR11978035.sra 2020-07-14T01:56:37 prefetch.2.10.7: 1) Downloading 'SRR11978036'... 2020-07-14T01:56:37 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:58:41 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:58:41 prefetch.2.10.7: 'SRR11978036' is valid 2020-07-14T01:58:41 prefetch.2.10.7: 1) 'SRR11978036' was downloaded successfully 2020-07-14T01:58:41 prefetch.2.10.7: 'SRR11978036' has 0 unresolved dependencies Read 9594368 spots for SRR11978036/SRR11978036.sra Written 9594368 spots for SRR11978036/SRR11978036.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627521 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:09:57 60728756 reads; of these: 60728756 (100.00%) were unpaired; of these: 51531951 (84.86%) aligned 0 times 6902753 (11.37%) aligned exactly 1 time 2294052 (3.78%) aligned >1 times 15.14% overall alignment rate Time searching: 00:09:58 Overall time: 00:09:58 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] 2122823 / 9196805 = 0.2308 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 11:12:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521334/SRX8521334.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521334/SRX8521334.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521334/SRX8521334.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521334/SRX8521334.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 11:12:59: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:12:59: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:13:06: 1000000 INFO @ Tue, 14 Jul 2020 11:13:13: 2000000 INFO @ Tue, 14 Jul 2020 11:13:20: 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 11:13:27: 4000000 INFO @ Tue, 14 Jul 2020 11:13:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521334/SRX8521334.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521334/SRX8521334.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521334/SRX8521334.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521334/SRX8521334.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 11:13:28: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:13:28: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:13:34: 5000000 INFO @ Tue, 14 Jul 2020 11:13:36: 1000000 INFO @ Tue, 14 Jul 2020 11:13:41: 6000000 INFO @ Tue, 14 Jul 2020 11:13:43: 2000000 INFO @ Tue, 14 Jul 2020 11:13:49: 7000000 INFO @ Tue, 14 Jul 2020 11:13:49: #1 tag size is determined as 70 bps INFO @ Tue, 14 Jul 2020 11:13:49: #1 tag size = 70 INFO @ Tue, 14 Jul 2020 11:13:49: #1 total tags in treatment: 7073982 INFO @ Tue, 14 Jul 2020 11:13:49: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:13:49: #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 11:13:49: #1 tags after filtering in treatment: 7073982 INFO @ Tue, 14 Jul 2020 11:13:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:13:49: #1 finished! INFO @ Tue, 14 Jul 2020 11:13:49: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:13:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:13:50: #2 number of paired peaks: 381 WARNING @ Tue, 14 Jul 2020 11:13:50: Fewer paired peaks (381) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 381 pairs to build model! INFO @ Tue, 14 Jul 2020 11:13:50: start model_add_line... INFO @ Tue, 14 Jul 2020 11:13:50: start X-correlation... INFO @ Tue, 14 Jul 2020 11:13:50: end of X-cor INFO @ Tue, 14 Jul 2020 11:13:50: #2 finished! INFO @ Tue, 14 Jul 2020 11:13:50: #2 predicted fragment length is 73 bps INFO @ Tue, 14 Jul 2020 11:13:50: #2 alternative fragment length(s) may be 73 bps INFO @ Tue, 14 Jul 2020 11:13:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521334/SRX8521334.05_model.r WARNING @ Tue, 14 Jul 2020 11:13:50: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:13:50: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Tue, 14 Jul 2020 11:13:50: #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 11:13:50: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:13:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:13:50: 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 11:13:57: 4000000 INFO @ Tue, 14 Jul 2020 11:13:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521334/SRX8521334.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521334/SRX8521334.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521334/SRX8521334.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521334/SRX8521334.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 11:13:58: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:13:58: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:14:04: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:14:04: 5000000 INFO @ Tue, 14 Jul 2020 11:14:06: 1000000 INFO @ Tue, 14 Jul 2020 11:14:12: 6000000 INFO @ Tue, 14 Jul 2020 11:14:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521334/SRX8521334.05_peaks.xls INFO @ Tue, 14 Jul 2020 11:14:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521334/SRX8521334.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:14:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521334/SRX8521334.05_summits.bed INFO @ Tue, 14 Jul 2020 11:14:12: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2079 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:14:13: 2000000 INFO @ Tue, 14 Jul 2020 11:14:19: 7000000 INFO @ Tue, 14 Jul 2020 11:14:19: #1 tag size is determined as 70 bps INFO @ Tue, 14 Jul 2020 11:14:19: #1 tag size = 70 INFO @ Tue, 14 Jul 2020 11:14:19: #1 total tags in treatment: 7073982 INFO @ Tue, 14 Jul 2020 11:14:19: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:14:19: #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 11:14:19: #1 tags after filtering in treatment: 7073982 INFO @ Tue, 14 Jul 2020 11:14:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:14:19: #1 finished! INFO @ Tue, 14 Jul 2020 11:14:19: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:14:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:14:20: #2 number of paired peaks: 381 WARNING @ Tue, 14 Jul 2020 11:14:20: Fewer paired peaks (381) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 381 pairs to build model! INFO @ Tue, 14 Jul 2020 11:14:20: start model_add_line... INFO @ Tue, 14 Jul 2020 11:14:20: start X-correlation... INFO @ Tue, 14 Jul 2020 11:14:20: end of X-cor INFO @ Tue, 14 Jul 2020 11:14:20: #2 finished! INFO @ Tue, 14 Jul 2020 11:14:20: #2 predicted fragment length is 73 bps INFO @ Tue, 14 Jul 2020 11:14:20: #2 alternative fragment length(s) may be 73 bps INFO @ Tue, 14 Jul 2020 11:14:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521334/SRX8521334.10_model.r WARNING @ Tue, 14 Jul 2020 11:14:20: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:14:20: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Tue, 14 Jul 2020 11:14:20: #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 11:14:20: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:14:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:14:21: 3000000 INFO @ Tue, 14 Jul 2020 11:14:28: 4000000 INFO @ Tue, 14 Jul 2020 11:14:34: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:14:34: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 11:14:42: 6000000 INFO @ Tue, 14 Jul 2020 11:14:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521334/SRX8521334.10_peaks.xls INFO @ Tue, 14 Jul 2020 11:14:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521334/SRX8521334.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:14:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521334/SRX8521334.10_summits.bed INFO @ Tue, 14 Jul 2020 11:14:42: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (844 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:14:49: 7000000 INFO @ Tue, 14 Jul 2020 11:14:49: #1 tag size is determined as 70 bps INFO @ Tue, 14 Jul 2020 11:14:49: #1 tag size = 70 INFO @ Tue, 14 Jul 2020 11:14:49: #1 total tags in treatment: 7073982 INFO @ Tue, 14 Jul 2020 11:14:49: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:14:49: #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 11:14:49: #1 tags after filtering in treatment: 7073982 INFO @ Tue, 14 Jul 2020 11:14:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:14:49: #1 finished! INFO @ Tue, 14 Jul 2020 11:14:49: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:14:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:14:50: #2 number of paired peaks: 381 WARNING @ Tue, 14 Jul 2020 11:14:50: Fewer paired peaks (381) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 381 pairs to build model! INFO @ Tue, 14 Jul 2020 11:14:50: start model_add_line... INFO @ Tue, 14 Jul 2020 11:14:50: start X-correlation... INFO @ Tue, 14 Jul 2020 11:14:50: end of X-cor INFO @ Tue, 14 Jul 2020 11:14:50: #2 finished! INFO @ Tue, 14 Jul 2020 11:14:50: #2 predicted fragment length is 73 bps INFO @ Tue, 14 Jul 2020 11:14:50: #2 alternative fragment length(s) may be 73 bps INFO @ Tue, 14 Jul 2020 11:14:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521334/SRX8521334.20_model.r WARNING @ Tue, 14 Jul 2020 11:14:50: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:14:50: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Tue, 14 Jul 2020 11:14:50: #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 11:14:50: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:14:50: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 11:15:05: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:15:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521334/SRX8521334.20_peaks.xls INFO @ Tue, 14 Jul 2020 11:15:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521334/SRX8521334.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:15:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521334/SRX8521334.20_summits.bed INFO @ Tue, 14 Jul 2020 11:15:12: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (245 records, 4 fields): 2 millis CompletedMACS2peakCalling