Job ID = 6627566 SRX = SRX8521404 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T03:01:33 prefetch.2.10.7: 1) Downloading 'SRR11978358'... 2020-07-14T03:01:33 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:03:09 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:03:10 prefetch.2.10.7: 'SRR11978358' is valid 2020-07-14T03:03:10 prefetch.2.10.7: 1) 'SRR11978358' was downloaded successfully 2020-07-14T03:03:10 prefetch.2.10.7: 'SRR11978358' has 0 unresolved dependencies Read 15548572 spots for SRR11978358/SRR11978358.sra Written 15548572 spots for SRR11978358/SRR11978358.sra 2020-07-14T03:04:17 prefetch.2.10.7: 1) Downloading 'SRR11978359'... 2020-07-14T03:04:17 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:05:35 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:05:36 prefetch.2.10.7: 'SRR11978359' is valid 2020-07-14T03:05:36 prefetch.2.10.7: 1) 'SRR11978359' was downloaded successfully 2020-07-14T03:05:36 prefetch.2.10.7: 'SRR11978359' has 0 unresolved dependencies Read 15348460 spots for SRR11978359/SRR11978359.sra Written 15348460 spots for SRR11978359/SRR11978359.sra 2020-07-14T03:06:41 prefetch.2.10.7: 1) Downloading 'SRR11978360'... 2020-07-14T03:06:41 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:08:19 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:08:20 prefetch.2.10.7: 'SRR11978360' is valid 2020-07-14T03:08:20 prefetch.2.10.7: 1) 'SRR11978360' was downloaded successfully 2020-07-14T03:08:20 prefetch.2.10.7: 'SRR11978360' has 0 unresolved dependencies Read 15562117 spots for SRR11978360/SRR11978360.sra Written 15562117 spots for SRR11978360/SRR11978360.sra 2020-07-14T03:09:30 prefetch.2.10.7: 1) Downloading 'SRR11978361'... 2020-07-14T03:09:30 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:18:40 prefetch.2.10.7: HTTPS download failed 2020-07-14T03:18:40 prefetch.2.10.7: 1) failed to download SRR11978361 2020-07-14T03:18:51 prefetch.2.10.7: 1) Downloading 'SRR11978361'... 2020-07-14T03:18:51 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:18:51 prefetch.2.10.7: Continue download of 'SRR11978361' from 423096226 2020-07-14T03:19:15 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:19:16 prefetch.2.10.7: 'SRR11978361' is valid 2020-07-14T03:19:16 prefetch.2.10.7: 1) 'SRR11978361' was downloaded successfully 2020-07-14T03:19:16 prefetch.2.10.7: 'SRR11978361' has 0 unresolved dependencies Read 15511685 spots for SRR11978361/SRR11978361.sra Written 15511685 spots for SRR11978361/SRR11978361.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627794 ("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: 00:08:45 61970834 reads; of these: 61970834 (100.00%) were unpaired; of these: 56237789 (90.75%) aligned 0 times 4337612 (7.00%) aligned exactly 1 time 1395433 (2.25%) aligned >1 times 9.25% overall alignment rate Time searching: 00:08:45 Overall time: 00:08:45 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] 1066726 / 5733045 = 0.1861 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 12:31:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521404/SRX8521404.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521404/SRX8521404.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521404/SRX8521404.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521404/SRX8521404.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 12:31:24: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:31:24: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:31:30: 1000000 INFO @ Tue, 14 Jul 2020 12:31:36: 2000000 INFO @ Tue, 14 Jul 2020 12:31:42: 3000000 INFO @ Tue, 14 Jul 2020 12:31:48: 4000000 INFO @ Tue, 14 Jul 2020 12:31:51: #1 tag size is determined as 58 bps INFO @ Tue, 14 Jul 2020 12:31:51: #1 tag size = 58 INFO @ Tue, 14 Jul 2020 12:31:51: #1 total tags in treatment: 4666319 INFO @ Tue, 14 Jul 2020 12:31:51: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:31:51: #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 12:31:52: #1 tags after filtering in treatment: 4666319 INFO @ Tue, 14 Jul 2020 12:31:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:31:52: #1 finished! INFO @ Tue, 14 Jul 2020 12:31:52: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:31:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:31:52: #2 number of paired peaks: 547 WARNING @ Tue, 14 Jul 2020 12:31:52: Fewer paired peaks (547) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 547 pairs to build model! INFO @ Tue, 14 Jul 2020 12:31:52: start model_add_line... INFO @ Tue, 14 Jul 2020 12:31:52: start X-correlation... INFO @ Tue, 14 Jul 2020 12:31:52: end of X-cor INFO @ Tue, 14 Jul 2020 12:31:52: #2 finished! INFO @ Tue, 14 Jul 2020 12:31:52: #2 predicted fragment length is 57 bps INFO @ Tue, 14 Jul 2020 12:31:52: #2 alternative fragment length(s) may be 57 bps INFO @ Tue, 14 Jul 2020 12:31:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521404/SRX8521404.05_model.r WARNING @ Tue, 14 Jul 2020 12:31:52: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:31:52: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Tue, 14 Jul 2020 12:31:52: #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 12:31:52: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:31:52: #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 12:31:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521404/SRX8521404.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521404/SRX8521404.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521404/SRX8521404.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521404/SRX8521404.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 12:31:55: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:31:55: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:32:01: 1000000 INFO @ Tue, 14 Jul 2020 12:32:03: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:32:08: 2000000 INFO @ Tue, 14 Jul 2020 12:32:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521404/SRX8521404.05_peaks.xls INFO @ Tue, 14 Jul 2020 12:32:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521404/SRX8521404.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:32:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521404/SRX8521404.05_summits.bed INFO @ Tue, 14 Jul 2020 12:32:08: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1897 records, 4 fields): 41 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 12:32:14: 3000000 INFO @ Tue, 14 Jul 2020 12:32:21: 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 12:32:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521404/SRX8521404.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521404/SRX8521404.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521404/SRX8521404.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521404/SRX8521404.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 12:32:24: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:32:24: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:32:25: #1 tag size is determined as 58 bps INFO @ Tue, 14 Jul 2020 12:32:25: #1 tag size = 58 INFO @ Tue, 14 Jul 2020 12:32:25: #1 total tags in treatment: 4666319 INFO @ Tue, 14 Jul 2020 12:32:25: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:32:25: #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 12:32:25: #1 tags after filtering in treatment: 4666319 INFO @ Tue, 14 Jul 2020 12:32:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:32:25: #1 finished! INFO @ Tue, 14 Jul 2020 12:32:25: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:32:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:32:25: #2 number of paired peaks: 547 WARNING @ Tue, 14 Jul 2020 12:32:25: Fewer paired peaks (547) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 547 pairs to build model! INFO @ Tue, 14 Jul 2020 12:32:25: start model_add_line... INFO @ Tue, 14 Jul 2020 12:32:25: start X-correlation... INFO @ Tue, 14 Jul 2020 12:32:26: end of X-cor INFO @ Tue, 14 Jul 2020 12:32:26: #2 finished! INFO @ Tue, 14 Jul 2020 12:32:26: #2 predicted fragment length is 57 bps INFO @ Tue, 14 Jul 2020 12:32:26: #2 alternative fragment length(s) may be 57 bps INFO @ Tue, 14 Jul 2020 12:32:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521404/SRX8521404.10_model.r WARNING @ Tue, 14 Jul 2020 12:32:26: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:32:26: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Tue, 14 Jul 2020 12:32:26: #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 12:32:26: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:32:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:32:31: 1000000 INFO @ Tue, 14 Jul 2020 12:32:36: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:32:38: 2000000 INFO @ Tue, 14 Jul 2020 12:32:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521404/SRX8521404.10_peaks.xls INFO @ Tue, 14 Jul 2020 12:32:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521404/SRX8521404.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:32:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521404/SRX8521404.10_summits.bed INFO @ Tue, 14 Jul 2020 12:32:41: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (683 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 12:32:45: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 12:32:51: 4000000 INFO @ Tue, 14 Jul 2020 12:32:56: #1 tag size is determined as 58 bps INFO @ Tue, 14 Jul 2020 12:32:56: #1 tag size = 58 INFO @ Tue, 14 Jul 2020 12:32:56: #1 total tags in treatment: 4666319 INFO @ Tue, 14 Jul 2020 12:32:56: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:32:56: #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 12:32:56: #1 tags after filtering in treatment: 4666319 INFO @ Tue, 14 Jul 2020 12:32:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:32:56: #1 finished! INFO @ Tue, 14 Jul 2020 12:32:56: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:32:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:32:56: #2 number of paired peaks: 547 WARNING @ Tue, 14 Jul 2020 12:32:56: Fewer paired peaks (547) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 547 pairs to build model! INFO @ Tue, 14 Jul 2020 12:32:56: start model_add_line... INFO @ Tue, 14 Jul 2020 12:32:56: start X-correlation... INFO @ Tue, 14 Jul 2020 12:32:56: end of X-cor INFO @ Tue, 14 Jul 2020 12:32:56: #2 finished! INFO @ Tue, 14 Jul 2020 12:32:56: #2 predicted fragment length is 57 bps INFO @ Tue, 14 Jul 2020 12:32:56: #2 alternative fragment length(s) may be 57 bps INFO @ Tue, 14 Jul 2020 12:32:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521404/SRX8521404.20_model.r WARNING @ Tue, 14 Jul 2020 12:32:56: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:32:56: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Tue, 14 Jul 2020 12:32:56: #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 12:32:56: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:32:56: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 12:33:07: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:33:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521404/SRX8521404.20_peaks.xls INFO @ Tue, 14 Jul 2020 12:33:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521404/SRX8521404.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:33:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521404/SRX8521404.20_summits.bed INFO @ Tue, 14 Jul 2020 12:33:12: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (140 records, 4 fields): 2 millis CompletedMACS2peakCalling