Job ID = 6627111 SRX = SRX8521289 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T00:56:17 prefetch.2.10.7: 1) Downloading 'SRR11978446'... 2020-07-14T00:56:17 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T00:57:57 prefetch.2.10.7: HTTPS download succeed 2020-07-14T00:57:58 prefetch.2.10.7: 'SRR11978446' is valid 2020-07-14T00:57:58 prefetch.2.10.7: 1) 'SRR11978446' was downloaded successfully 2020-07-14T00:57:58 prefetch.2.10.7: 'SRR11978446' has 0 unresolved dependencies Read 13263610 spots for SRR11978446/SRR11978446.sra Written 13263610 spots for SRR11978446/SRR11978446.sra 2020-07-14T00:58:51 prefetch.2.10.7: 1) Downloading 'SRR11978447'... 2020-07-14T00:58:51 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:00:28 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:00:29 prefetch.2.10.7: 'SRR11978447' is valid 2020-07-14T01:00:29 prefetch.2.10.7: 1) 'SRR11978447' was downloaded successfully 2020-07-14T01:00:29 prefetch.2.10.7: 'SRR11978447' has 0 unresolved dependencies Read 13058100 spots for SRR11978447/SRR11978447.sra Written 13058100 spots for SRR11978447/SRR11978447.sra 2020-07-14T01:01:21 prefetch.2.10.7: 1) Downloading 'SRR11978448'... 2020-07-14T01:01:21 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:03:16 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:03:17 prefetch.2.10.7: 'SRR11978448' is valid 2020-07-14T01:03:17 prefetch.2.10.7: 1) 'SRR11978448' was downloaded successfully 2020-07-14T01:03:17 prefetch.2.10.7: 'SRR11978448' has 0 unresolved dependencies Read 13482246 spots for SRR11978448/SRR11978448.sra Written 13482246 spots for SRR11978448/SRR11978448.sra 2020-07-14T01:04:17 prefetch.2.10.7: 1) Downloading 'SRR11978449'... 2020-07-14T01:04:17 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:08:32 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:08:33 prefetch.2.10.7: 'SRR11978449' is valid 2020-07-14T01:08:33 prefetch.2.10.7: 1) 'SRR11978449' was downloaded successfully 2020-07-14T01:08:33 prefetch.2.10.7: 'SRR11978449' has 0 unresolved dependencies Read 13348001 spots for SRR11978449/SRR11978449.sra Written 13348001 spots for SRR11978449/SRR11978449.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627351 ("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: 00:07:36 53151957 reads; of these: 53151957 (100.00%) were unpaired; of these: 45019154 (84.70%) aligned 0 times 6250286 (11.76%) aligned exactly 1 time 1882517 (3.54%) aligned >1 times 15.30% overall alignment rate Time searching: 00:07:36 Overall time: 00:07:36 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] 1798413 / 8132803 = 0.2211 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 10:19:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521289/SRX8521289.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521289/SRX8521289.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521289/SRX8521289.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521289/SRX8521289.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 10:19:46: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:19:46: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:19:52: 1000000 INFO @ Tue, 14 Jul 2020 10:19:58: 2000000 INFO @ Tue, 14 Jul 2020 10:20:03: 3000000 INFO @ Tue, 14 Jul 2020 10:20:09: 4000000 INFO @ Tue, 14 Jul 2020 10:20:15: 5000000 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 10:20:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521289/SRX8521289.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521289/SRX8521289.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521289/SRX8521289.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521289/SRX8521289.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 10:20:16: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:20:16: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:20:21: 6000000 INFO @ Tue, 14 Jul 2020 10:20:22: 1000000 INFO @ Tue, 14 Jul 2020 10:20:23: #1 tag size is determined as 58 bps INFO @ Tue, 14 Jul 2020 10:20:23: #1 tag size = 58 INFO @ Tue, 14 Jul 2020 10:20:23: #1 total tags in treatment: 6334390 INFO @ Tue, 14 Jul 2020 10:20:23: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:20:23: #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 10:20:23: #1 tags after filtering in treatment: 6334390 INFO @ Tue, 14 Jul 2020 10:20:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:20:23: #1 finished! INFO @ Tue, 14 Jul 2020 10:20:23: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:20:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:20:23: #2 number of paired peaks: 399 WARNING @ Tue, 14 Jul 2020 10:20:23: Fewer paired peaks (399) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 399 pairs to build model! INFO @ Tue, 14 Jul 2020 10:20:23: start model_add_line... INFO @ Tue, 14 Jul 2020 10:20:23: start X-correlation... INFO @ Tue, 14 Jul 2020 10:20:23: end of X-cor INFO @ Tue, 14 Jul 2020 10:20:23: #2 finished! INFO @ Tue, 14 Jul 2020 10:20:23: #2 predicted fragment length is 60 bps INFO @ Tue, 14 Jul 2020 10:20:23: #2 alternative fragment length(s) may be 60 bps INFO @ Tue, 14 Jul 2020 10:20:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521289/SRX8521289.05_model.r WARNING @ Tue, 14 Jul 2020 10:20:23: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:20:23: #2 You may need to consider one of the other alternative d(s): 60 WARNING @ Tue, 14 Jul 2020 10:20:23: #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 10:20:23: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:20:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:20:28: 2000000 INFO @ Tue, 14 Jul 2020 10:20:34: 3000000 INFO @ Tue, 14 Jul 2020 10:20:37: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:20:40: 4000000 INFO @ Tue, 14 Jul 2020 10:20:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521289/SRX8521289.05_peaks.xls INFO @ Tue, 14 Jul 2020 10:20:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521289/SRX8521289.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:20:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521289/SRX8521289.05_summits.bed INFO @ Tue, 14 Jul 2020 10:20:43: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2554 records, 4 fields): 5 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 10:20:46: 5000000 INFO @ Tue, 14 Jul 2020 10:20:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521289/SRX8521289.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521289/SRX8521289.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521289/SRX8521289.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521289/SRX8521289.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 10:20:46: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:20:46: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:20:52: 6000000 INFO @ Tue, 14 Jul 2020 10:20:52: 1000000 INFO @ Tue, 14 Jul 2020 10:20:54: #1 tag size is determined as 58 bps INFO @ Tue, 14 Jul 2020 10:20:54: #1 tag size = 58 INFO @ Tue, 14 Jul 2020 10:20:54: #1 total tags in treatment: 6334390 INFO @ Tue, 14 Jul 2020 10:20:54: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:20:54: #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 10:20:54: #1 tags after filtering in treatment: 6334390 INFO @ Tue, 14 Jul 2020 10:20:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:20:54: #1 finished! INFO @ Tue, 14 Jul 2020 10:20:54: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:20:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:20:54: #2 number of paired peaks: 399 WARNING @ Tue, 14 Jul 2020 10:20:54: Fewer paired peaks (399) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 399 pairs to build model! INFO @ Tue, 14 Jul 2020 10:20:54: start model_add_line... INFO @ Tue, 14 Jul 2020 10:20:54: start X-correlation... INFO @ Tue, 14 Jul 2020 10:20:54: end of X-cor INFO @ Tue, 14 Jul 2020 10:20:54: #2 finished! INFO @ Tue, 14 Jul 2020 10:20:54: #2 predicted fragment length is 60 bps INFO @ Tue, 14 Jul 2020 10:20:54: #2 alternative fragment length(s) may be 60 bps INFO @ Tue, 14 Jul 2020 10:20:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521289/SRX8521289.10_model.r WARNING @ Tue, 14 Jul 2020 10:20:54: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:20:54: #2 You may need to consider one of the other alternative d(s): 60 WARNING @ Tue, 14 Jul 2020 10:20:54: #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 10:20:54: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:20:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:20:58: 2000000 INFO @ Tue, 14 Jul 2020 10:21:04: 3000000 INFO @ Tue, 14 Jul 2020 10:21:08: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:21:10: 4000000 INFO @ Tue, 14 Jul 2020 10:21:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521289/SRX8521289.10_peaks.xls INFO @ Tue, 14 Jul 2020 10:21:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521289/SRX8521289.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:21:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521289/SRX8521289.10_summits.bed INFO @ Tue, 14 Jul 2020 10:21:14: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (868 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:21:16: 5000000 INFO @ Tue, 14 Jul 2020 10:21:21: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 10:21:23: #1 tag size is determined as 58 bps INFO @ Tue, 14 Jul 2020 10:21:23: #1 tag size = 58 INFO @ Tue, 14 Jul 2020 10:21:23: #1 total tags in treatment: 6334390 INFO @ Tue, 14 Jul 2020 10:21:23: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:21:23: #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 10:21:23: #1 tags after filtering in treatment: 6334390 INFO @ Tue, 14 Jul 2020 10:21:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:21:23: #1 finished! INFO @ Tue, 14 Jul 2020 10:21:23: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:21:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:21:24: #2 number of paired peaks: 399 WARNING @ Tue, 14 Jul 2020 10:21:24: Fewer paired peaks (399) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 399 pairs to build model! INFO @ Tue, 14 Jul 2020 10:21:24: start model_add_line... INFO @ Tue, 14 Jul 2020 10:21:24: start X-correlation... INFO @ Tue, 14 Jul 2020 10:21:24: end of X-cor INFO @ Tue, 14 Jul 2020 10:21:24: #2 finished! INFO @ Tue, 14 Jul 2020 10:21:24: #2 predicted fragment length is 60 bps INFO @ Tue, 14 Jul 2020 10:21:24: #2 alternative fragment length(s) may be 60 bps INFO @ Tue, 14 Jul 2020 10:21:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521289/SRX8521289.20_model.r WARNING @ Tue, 14 Jul 2020 10:21:24: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:21:24: #2 You may need to consider one of the other alternative d(s): 60 WARNING @ Tue, 14 Jul 2020 10:21:24: #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 10:21:24: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:21:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:21:37: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 10:21:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521289/SRX8521289.20_peaks.xls INFO @ Tue, 14 Jul 2020 10:21:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521289/SRX8521289.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:21:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521289/SRX8521289.20_summits.bed INFO @ Tue, 14 Jul 2020 10:21:44: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (207 records, 4 fields): 1 millis CompletedMACS2peakCalling