Job ID = 6627251 SRX = SRX8521325 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T01:36:56 prefetch.2.10.7: 1) Downloading 'SRR11977969'... 2020-07-14T01:36:56 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:38:14 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:38:15 prefetch.2.10.7: 'SRR11977969' is valid 2020-07-14T01:38:15 prefetch.2.10.7: 1) 'SRR11977969' was downloaded successfully 2020-07-14T01:38:15 prefetch.2.10.7: 'SRR11977969' has 0 unresolved dependencies Read 8905732 spots for SRR11977969/SRR11977969.sra Written 8905732 spots for SRR11977969/SRR11977969.sra 2020-07-14T01:38:54 prefetch.2.10.7: 1) Downloading 'SRR11977970'... 2020-07-14T01:38:54 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:40:23 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:40:24 prefetch.2.10.7: 'SRR11977970' is valid 2020-07-14T01:40:24 prefetch.2.10.7: 1) 'SRR11977970' was downloaded successfully 2020-07-14T01:40:24 prefetch.2.10.7: 'SRR11977970' has 0 unresolved dependencies Read 8804044 spots for SRR11977970/SRR11977970.sra Written 8804044 spots for SRR11977970/SRR11977970.sra 2020-07-14T01:41:03 prefetch.2.10.7: 1) Downloading 'SRR11977971'... 2020-07-14T01:41:03 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:42:01 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:42:02 prefetch.2.10.7: 'SRR11977971' is valid 2020-07-14T01:42:02 prefetch.2.10.7: 1) 'SRR11977971' was downloaded successfully 2020-07-14T01:42:02 prefetch.2.10.7: 'SRR11977971' has 0 unresolved dependencies Read 8810688 spots for SRR11977971/SRR11977971.sra Written 8810688 spots for SRR11977971/SRR11977971.sra 2020-07-14T01:42:45 prefetch.2.10.7: 1) Downloading 'SRR11977972'... 2020-07-14T01:42:45 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:43:52 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:43:53 prefetch.2.10.7: 'SRR11977972' is valid 2020-07-14T01:43:53 prefetch.2.10.7: 1) 'SRR11977972' was downloaded successfully 2020-07-14T01:43:53 prefetch.2.10.7: 'SRR11977972' has 0 unresolved dependencies Read 9071326 spots for SRR11977972/SRR11977972.sra Written 9071326 spots for SRR11977972/SRR11977972.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627446 ("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: 00:05:02 35591790 reads; of these: 35591790 (100.00%) were unpaired; of these: 32100370 (90.19%) aligned 0 times 2682241 (7.54%) aligned exactly 1 time 809179 (2.27%) aligned >1 times 9.81% overall alignment rate Time searching: 00:05:02 Overall time: 00:05:02 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] 557992 / 3491420 = 0.1598 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 10:51:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521325/SRX8521325.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521325/SRX8521325.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521325/SRX8521325.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521325/SRX8521325.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 10:51:01: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:51:01: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:51:08: 1000000 INFO @ Tue, 14 Jul 2020 10:51:15: 2000000 INFO @ Tue, 14 Jul 2020 10:51:22: #1 tag size is determined as 54 bps INFO @ Tue, 14 Jul 2020 10:51:22: #1 tag size = 54 INFO @ Tue, 14 Jul 2020 10:51:22: #1 total tags in treatment: 2933428 INFO @ Tue, 14 Jul 2020 10:51:22: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:51:22: #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 10:51:22: #1 tags after filtering in treatment: 2933428 INFO @ Tue, 14 Jul 2020 10:51:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:51:22: #1 finished! INFO @ Tue, 14 Jul 2020 10:51:22: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:51:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:51:22: #2 number of paired peaks: 593 WARNING @ Tue, 14 Jul 2020 10:51:22: Fewer paired peaks (593) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 593 pairs to build model! INFO @ Tue, 14 Jul 2020 10:51:22: start model_add_line... INFO @ Tue, 14 Jul 2020 10:51:22: start X-correlation... INFO @ Tue, 14 Jul 2020 10:51:22: end of X-cor INFO @ Tue, 14 Jul 2020 10:51:22: #2 finished! INFO @ Tue, 14 Jul 2020 10:51:22: #2 predicted fragment length is 62 bps INFO @ Tue, 14 Jul 2020 10:51:22: #2 alternative fragment length(s) may be 62 bps INFO @ Tue, 14 Jul 2020 10:51:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521325/SRX8521325.05_model.r WARNING @ Tue, 14 Jul 2020 10:51:22: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:51:22: #2 You may need to consider one of the other alternative d(s): 62 WARNING @ Tue, 14 Jul 2020 10:51:22: #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 10:51:22: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:51:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:51:28: #3 Call peaks for each chromosome... 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 10:51:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521325/SRX8521325.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521325/SRX8521325.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521325/SRX8521325.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521325/SRX8521325.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 10:51:31: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:51:31: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:51:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521325/SRX8521325.05_peaks.xls INFO @ Tue, 14 Jul 2020 10:51:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521325/SRX8521325.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:51:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521325/SRX8521325.05_summits.bed INFO @ Tue, 14 Jul 2020 10:51:32: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1281 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:51:37: 1000000 INFO @ Tue, 14 Jul 2020 10:51:44: 2000000 INFO @ Tue, 14 Jul 2020 10:51:49: #1 tag size is determined as 54 bps INFO @ Tue, 14 Jul 2020 10:51:49: #1 tag size = 54 INFO @ Tue, 14 Jul 2020 10:51:49: #1 total tags in treatment: 2933428 INFO @ Tue, 14 Jul 2020 10:51:49: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:51:49: #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 10:51:49: #1 tags after filtering in treatment: 2933428 INFO @ Tue, 14 Jul 2020 10:51:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:51:49: #1 finished! INFO @ Tue, 14 Jul 2020 10:51:49: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:51:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:51:49: #2 number of paired peaks: 593 WARNING @ Tue, 14 Jul 2020 10:51:49: Fewer paired peaks (593) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 593 pairs to build model! INFO @ Tue, 14 Jul 2020 10:51:49: start model_add_line... INFO @ Tue, 14 Jul 2020 10:51:49: start X-correlation... INFO @ Tue, 14 Jul 2020 10:51:49: end of X-cor INFO @ Tue, 14 Jul 2020 10:51:49: #2 finished! INFO @ Tue, 14 Jul 2020 10:51:49: #2 predicted fragment length is 62 bps INFO @ Tue, 14 Jul 2020 10:51:49: #2 alternative fragment length(s) may be 62 bps INFO @ Tue, 14 Jul 2020 10:51:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521325/SRX8521325.10_model.r WARNING @ Tue, 14 Jul 2020 10:51:49: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:51:49: #2 You may need to consider one of the other alternative d(s): 62 WARNING @ Tue, 14 Jul 2020 10:51:49: #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 10:51:49: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:51:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:51:56: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:51:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521325/SRX8521325.10_peaks.xls INFO @ Tue, 14 Jul 2020 10:51:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521325/SRX8521325.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:51:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521325/SRX8521325.10_summits.bed INFO @ Tue, 14 Jul 2020 10:51:59: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (432 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 10:52:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521325/SRX8521325.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521325/SRX8521325.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521325/SRX8521325.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521325/SRX8521325.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 10:52:01: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:52:01: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:52:08: 1000000 INFO @ Tue, 14 Jul 2020 10:52:14: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 10:52:20: #1 tag size is determined as 54 bps INFO @ Tue, 14 Jul 2020 10:52:20: #1 tag size = 54 INFO @ Tue, 14 Jul 2020 10:52:20: #1 total tags in treatment: 2933428 INFO @ Tue, 14 Jul 2020 10:52:20: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:52:20: #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 10:52:20: #1 tags after filtering in treatment: 2933428 INFO @ Tue, 14 Jul 2020 10:52:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:52:20: #1 finished! INFO @ Tue, 14 Jul 2020 10:52:20: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:52:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:52:20: #2 number of paired peaks: 593 WARNING @ Tue, 14 Jul 2020 10:52:20: Fewer paired peaks (593) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 593 pairs to build model! INFO @ Tue, 14 Jul 2020 10:52:20: start model_add_line... INFO @ Tue, 14 Jul 2020 10:52:20: start X-correlation... INFO @ Tue, 14 Jul 2020 10:52:20: end of X-cor INFO @ Tue, 14 Jul 2020 10:52:20: #2 finished! INFO @ Tue, 14 Jul 2020 10:52:20: #2 predicted fragment length is 62 bps INFO @ Tue, 14 Jul 2020 10:52:20: #2 alternative fragment length(s) may be 62 bps INFO @ Tue, 14 Jul 2020 10:52:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521325/SRX8521325.20_model.r WARNING @ Tue, 14 Jul 2020 10:52:20: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:52:20: #2 You may need to consider one of the other alternative d(s): 62 WARNING @ Tue, 14 Jul 2020 10:52:20: #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 10:52:20: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:52:20: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 10:52:27: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:52:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521325/SRX8521325.20_peaks.xls INFO @ Tue, 14 Jul 2020 10:52:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521325/SRX8521325.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:52:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521325/SRX8521325.20_summits.bed INFO @ Tue, 14 Jul 2020 10:52:30: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (93 records, 4 fields): 1 millis CompletedMACS2peakCalling