Job ID = 6627256 SRX = SRX8521328 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T01:37:30 prefetch.2.10.7: 1) Downloading 'SRR11977981'... 2020-07-14T01:37:30 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:38:21 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:38:21 prefetch.2.10.7: 'SRR11977981' is valid 2020-07-14T01:38:21 prefetch.2.10.7: 1) 'SRR11977981' was downloaded successfully 2020-07-14T01:38:21 prefetch.2.10.7: 'SRR11977981' has 0 unresolved dependencies Read 9627365 spots for SRR11977981/SRR11977981.sra Written 9627365 spots for SRR11977981/SRR11977981.sra 2020-07-14T01:39:03 prefetch.2.10.7: 1) Downloading 'SRR11977982'... 2020-07-14T01:39:03 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:40:32 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:40:33 prefetch.2.10.7: 'SRR11977982' is valid 2020-07-14T01:40:33 prefetch.2.10.7: 1) 'SRR11977982' was downloaded successfully 2020-07-14T01:40:33 prefetch.2.10.7: 'SRR11977982' has 0 unresolved dependencies Read 9561797 spots for SRR11977982/SRR11977982.sra Written 9561797 spots for SRR11977982/SRR11977982.sra 2020-07-14T01:41:18 prefetch.2.10.7: 1) Downloading 'SRR11977983'... 2020-07-14T01:41:18 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:42:27 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:42:28 prefetch.2.10.7: 'SRR11977983' is valid 2020-07-14T01:42:28 prefetch.2.10.7: 1) 'SRR11977983' was downloaded successfully 2020-07-14T01:42:28 prefetch.2.10.7: 'SRR11977983' has 0 unresolved dependencies Read 9616569 spots for SRR11977983/SRR11977983.sra Written 9616569 spots for SRR11977983/SRR11977983.sra 2020-07-14T01:43:22 prefetch.2.10.7: 1) Downloading 'SRR11977984'... 2020-07-14T01:43:22 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:44:48 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:44:48 prefetch.2.10.7: 'SRR11977984' is valid 2020-07-14T01:44:48 prefetch.2.10.7: 1) 'SRR11977984' was downloaded successfully 2020-07-14T01:44:48 prefetch.2.10.7: 'SRR11977984' has 0 unresolved dependencies Read 9892645 spots for SRR11977984/SRR11977984.sra Written 9892645 spots for SRR11977984/SRR11977984.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627454 ("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: 00:05:39 38698376 reads; of these: 38698376 (100.00%) were unpaired; of these: 33255493 (85.94%) aligned 0 times 4225714 (10.92%) aligned exactly 1 time 1217169 (3.15%) aligned >1 times 14.06% overall alignment rate Time searching: 00:05:40 Overall time: 00:05:40 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] 935350 / 5442883 = 0.1718 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 10:53:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521328/SRX8521328.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521328/SRX8521328.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521328/SRX8521328.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521328/SRX8521328.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 10:53:17: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:53:17: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:53:23: 1000000 INFO @ Tue, 14 Jul 2020 10:53:29: 2000000 INFO @ Tue, 14 Jul 2020 10:53:35: 3000000 INFO @ Tue, 14 Jul 2020 10:53:41: 4000000 INFO @ Tue, 14 Jul 2020 10:53:44: #1 tag size is determined as 67 bps INFO @ Tue, 14 Jul 2020 10:53:44: #1 tag size = 67 INFO @ Tue, 14 Jul 2020 10:53:44: #1 total tags in treatment: 4507533 INFO @ Tue, 14 Jul 2020 10:53:44: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:53:44: #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 10:53:44: #1 tags after filtering in treatment: 4507533 INFO @ Tue, 14 Jul 2020 10:53:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:53:44: #1 finished! INFO @ Tue, 14 Jul 2020 10:53:44: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:53:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:53:44: #2 number of paired peaks: 527 WARNING @ Tue, 14 Jul 2020 10:53:44: Fewer paired peaks (527) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 527 pairs to build model! INFO @ Tue, 14 Jul 2020 10:53:44: start model_add_line... INFO @ Tue, 14 Jul 2020 10:53:44: start X-correlation... INFO @ Tue, 14 Jul 2020 10:53:44: end of X-cor INFO @ Tue, 14 Jul 2020 10:53:44: #2 finished! INFO @ Tue, 14 Jul 2020 10:53:44: #2 predicted fragment length is 56 bps INFO @ Tue, 14 Jul 2020 10:53:44: #2 alternative fragment length(s) may be 56 bps INFO @ Tue, 14 Jul 2020 10:53:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521328/SRX8521328.05_model.r WARNING @ Tue, 14 Jul 2020 10:53:44: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:53:44: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Tue, 14 Jul 2020 10:53:44: #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 10:53:44: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:53:44: #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 10:53:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521328/SRX8521328.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521328/SRX8521328.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521328/SRX8521328.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521328/SRX8521328.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 10:53:47: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:53:47: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:53:53: 1000000 INFO @ Tue, 14 Jul 2020 10:53:54: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:53:59: 2000000 INFO @ Tue, 14 Jul 2020 10:54:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521328/SRX8521328.05_peaks.xls INFO @ Tue, 14 Jul 2020 10:54:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521328/SRX8521328.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:54:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521328/SRX8521328.05_summits.bed INFO @ Tue, 14 Jul 2020 10:54:00: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1819 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:54:06: 3000000 INFO @ Tue, 14 Jul 2020 10:54:12: 4000000 INFO @ Tue, 14 Jul 2020 10:54:15: #1 tag size is determined as 67 bps INFO @ Tue, 14 Jul 2020 10:54:15: #1 tag size = 67 INFO @ Tue, 14 Jul 2020 10:54:15: #1 total tags in treatment: 4507533 INFO @ Tue, 14 Jul 2020 10:54:15: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:54:15: #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 10:54:15: #1 tags after filtering in treatment: 4507533 INFO @ Tue, 14 Jul 2020 10:54:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:54:15: #1 finished! INFO @ Tue, 14 Jul 2020 10:54:15: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:54:15: #2 looking for paired plus/minus strand peaks... 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 10:54:15: #2 number of paired peaks: 527 WARNING @ Tue, 14 Jul 2020 10:54:15: Fewer paired peaks (527) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 527 pairs to build model! INFO @ Tue, 14 Jul 2020 10:54:15: start model_add_line... INFO @ Tue, 14 Jul 2020 10:54:15: start X-correlation... INFO @ Tue, 14 Jul 2020 10:54:15: end of X-cor INFO @ Tue, 14 Jul 2020 10:54:15: #2 finished! INFO @ Tue, 14 Jul 2020 10:54:15: #2 predicted fragment length is 56 bps INFO @ Tue, 14 Jul 2020 10:54:15: #2 alternative fragment length(s) may be 56 bps INFO @ Tue, 14 Jul 2020 10:54:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521328/SRX8521328.10_model.r WARNING @ Tue, 14 Jul 2020 10:54:15: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:54:15: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Tue, 14 Jul 2020 10:54:15: #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 10:54:15: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:54:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:54:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521328/SRX8521328.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521328/SRX8521328.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521328/SRX8521328.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521328/SRX8521328.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 10:54:17: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:54:17: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:54:23: 1000000 INFO @ Tue, 14 Jul 2020 10:54:26: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:54:29: 2000000 INFO @ Tue, 14 Jul 2020 10:54:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521328/SRX8521328.10_peaks.xls INFO @ Tue, 14 Jul 2020 10:54:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521328/SRX8521328.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:54:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521328/SRX8521328.10_summits.bed INFO @ Tue, 14 Jul 2020 10:54:31: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (770 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:54:35: 3000000 INFO @ Tue, 14 Jul 2020 10:54:40: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 10:54:43: #1 tag size is determined as 67 bps INFO @ Tue, 14 Jul 2020 10:54:43: #1 tag size = 67 INFO @ Tue, 14 Jul 2020 10:54:43: #1 total tags in treatment: 4507533 INFO @ Tue, 14 Jul 2020 10:54:43: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:54:43: #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 10:54:44: #1 tags after filtering in treatment: 4507533 INFO @ Tue, 14 Jul 2020 10:54:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:54:44: #1 finished! INFO @ Tue, 14 Jul 2020 10:54:44: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:54:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:54:44: #2 number of paired peaks: 527 WARNING @ Tue, 14 Jul 2020 10:54:44: Fewer paired peaks (527) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 527 pairs to build model! INFO @ Tue, 14 Jul 2020 10:54:44: start model_add_line... INFO @ Tue, 14 Jul 2020 10:54:44: start X-correlation... INFO @ Tue, 14 Jul 2020 10:54:44: end of X-cor INFO @ Tue, 14 Jul 2020 10:54:44: #2 finished! INFO @ Tue, 14 Jul 2020 10:54:44: #2 predicted fragment length is 56 bps INFO @ Tue, 14 Jul 2020 10:54:44: #2 alternative fragment length(s) may be 56 bps INFO @ Tue, 14 Jul 2020 10:54:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521328/SRX8521328.20_model.r WARNING @ Tue, 14 Jul 2020 10:54:44: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:54:44: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Tue, 14 Jul 2020 10:54:44: #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 10:54:44: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:54:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:54:55: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 10:55:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521328/SRX8521328.20_peaks.xls INFO @ Tue, 14 Jul 2020 10:55:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521328/SRX8521328.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:55:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521328/SRX8521328.20_summits.bed INFO @ Tue, 14 Jul 2020 10:55:01: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (141 records, 4 fields): 1 millis CompletedMACS2peakCalling