Job ID = 6627248 SRX = SRX8521323 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T01:36:31 prefetch.2.10.7: 1) Downloading 'SRR11977961'... 2020-07-14T01:36:31 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:37:36 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:37:36 prefetch.2.10.7: 'SRR11977961' is valid 2020-07-14T01:37:36 prefetch.2.10.7: 1) 'SRR11977961' was downloaded successfully 2020-07-14T01:37:36 prefetch.2.10.7: 'SRR11977961' has 0 unresolved dependencies Read 10470016 spots for SRR11977961/SRR11977961.sra Written 10470016 spots for SRR11977961/SRR11977961.sra 2020-07-14T01:38:20 prefetch.2.10.7: 1) Downloading 'SRR11977962'... 2020-07-14T01:38:20 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:39:38 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:39:39 prefetch.2.10.7: 'SRR11977962' is valid 2020-07-14T01:39:39 prefetch.2.10.7: 1) 'SRR11977962' was downloaded successfully 2020-07-14T01:39:39 prefetch.2.10.7: 'SRR11977962' has 0 unresolved dependencies Read 10342935 spots for SRR11977962/SRR11977962.sra Written 10342935 spots for SRR11977962/SRR11977962.sra 2020-07-14T01:40:22 prefetch.2.10.7: 1) Downloading 'SRR11977963'... 2020-07-14T01:40:22 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:41:49 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:41:50 prefetch.2.10.7: 'SRR11977963' is valid 2020-07-14T01:41:50 prefetch.2.10.7: 1) 'SRR11977963' was downloaded successfully 2020-07-14T01:41:50 prefetch.2.10.7: 'SRR11977963' has 0 unresolved dependencies Read 10450389 spots for SRR11977963/SRR11977963.sra Written 10450389 spots for SRR11977963/SRR11977963.sra 2020-07-14T01:42:38 prefetch.2.10.7: 1) Downloading 'SRR11977964'... 2020-07-14T01:42:38 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:44:47 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:44:47 prefetch.2.10.7: 'SRR11977964' is valid 2020-07-14T01:44:47 prefetch.2.10.7: 1) 'SRR11977964' was downloaded successfully 2020-07-14T01:44:47 prefetch.2.10.7: 'SRR11977964' has 0 unresolved dependencies Read 10771828 spots for SRR11977964/SRR11977964.sra Written 10771828 spots for SRR11977964/SRR11977964.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627455 ("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: 00:05:43 42035168 reads; of these: 42035168 (100.00%) were unpaired; of these: 37367818 (88.90%) aligned 0 times 3570069 (8.49%) aligned exactly 1 time 1097281 (2.61%) aligned >1 times 11.10% overall alignment rate Time searching: 00:05:43 Overall time: 00:05:43 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] 766876 / 4667350 = 0.1643 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 10:53:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521323/SRX8521323.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521323/SRX8521323.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521323/SRX8521323.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521323/SRX8521323.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 10:53:01: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:53:01: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:53:07: 1000000 INFO @ Tue, 14 Jul 2020 10:53:13: 2000000 INFO @ Tue, 14 Jul 2020 10:53:19: 3000000 INFO @ Tue, 14 Jul 2020 10:53:24: #1 tag size is determined as 59 bps INFO @ Tue, 14 Jul 2020 10:53:24: #1 tag size = 59 INFO @ Tue, 14 Jul 2020 10:53:24: #1 total tags in treatment: 3900474 INFO @ Tue, 14 Jul 2020 10:53:24: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:53:24: #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 10:53:24: #1 tags after filtering in treatment: 3900474 INFO @ Tue, 14 Jul 2020 10:53:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:53:24: #1 finished! INFO @ Tue, 14 Jul 2020 10:53:24: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:53:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:53:24: #2 number of paired peaks: 571 WARNING @ Tue, 14 Jul 2020 10:53:24: Fewer paired peaks (571) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 571 pairs to build model! INFO @ Tue, 14 Jul 2020 10:53:24: start model_add_line... INFO @ Tue, 14 Jul 2020 10:53:24: start X-correlation... INFO @ Tue, 14 Jul 2020 10:53:24: end of X-cor INFO @ Tue, 14 Jul 2020 10:53:24: #2 finished! INFO @ Tue, 14 Jul 2020 10:53:24: #2 predicted fragment length is 56 bps INFO @ Tue, 14 Jul 2020 10:53:24: #2 alternative fragment length(s) may be 56 bps INFO @ Tue, 14 Jul 2020 10:53:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521323/SRX8521323.05_model.r WARNING @ Tue, 14 Jul 2020 10:53:24: #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 10:53:24: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Tue, 14 Jul 2020 10:53:24: #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 10:53:24: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:53:24: #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 10:53:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521323/SRX8521323.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521323/SRX8521323.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521323/SRX8521323.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521323/SRX8521323.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 10:53:31: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:53:31: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:53:33: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:53:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521323/SRX8521323.05_peaks.xls INFO @ Tue, 14 Jul 2020 10:53:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521323/SRX8521323.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:53:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521323/SRX8521323.05_summits.bed INFO @ Tue, 14 Jul 2020 10:53:37: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1691 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:53:39: 1000000 INFO @ Tue, 14 Jul 2020 10:53:46: 2000000 INFO @ Tue, 14 Jul 2020 10:53:54: 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 10:54:01: #1 tag size is determined as 59 bps INFO @ Tue, 14 Jul 2020 10:54:01: #1 tag size = 59 INFO @ Tue, 14 Jul 2020 10:54:01: #1 total tags in treatment: 3900474 INFO @ Tue, 14 Jul 2020 10:54:01: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:54:01: #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 10:54:01: #1 tags after filtering in treatment: 3900474 INFO @ Tue, 14 Jul 2020 10:54:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:54:01: #1 finished! INFO @ Tue, 14 Jul 2020 10:54:01: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:54:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:54:01: #2 number of paired peaks: 571 WARNING @ Tue, 14 Jul 2020 10:54:01: Fewer paired peaks (571) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 571 pairs to build model! INFO @ Tue, 14 Jul 2020 10:54:01: start model_add_line... INFO @ Tue, 14 Jul 2020 10:54:01: start X-correlation... INFO @ Tue, 14 Jul 2020 10:54:01: end of X-cor INFO @ Tue, 14 Jul 2020 10:54:01: #2 finished! INFO @ Tue, 14 Jul 2020 10:54:01: #2 predicted fragment length is 56 bps INFO @ Tue, 14 Jul 2020 10:54:01: #2 alternative fragment length(s) may be 56 bps INFO @ Tue, 14 Jul 2020 10:54:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521323/SRX8521323.10_model.r WARNING @ Tue, 14 Jul 2020 10:54:01: #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 10:54:01: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Tue, 14 Jul 2020 10:54:01: #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 10:54:01: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:54:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:54:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521323/SRX8521323.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521323/SRX8521323.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521323/SRX8521323.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521323/SRX8521323.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 10:54:01: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:54:01: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:54:07: 1000000 INFO @ Tue, 14 Jul 2020 10:54:10: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:54:13: 2000000 INFO @ Tue, 14 Jul 2020 10:54:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521323/SRX8521323.10_peaks.xls INFO @ Tue, 14 Jul 2020 10:54:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521323/SRX8521323.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:54:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521323/SRX8521323.10_summits.bed INFO @ Tue, 14 Jul 2020 10:54:14: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (698 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:54:19: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 10:54:24: #1 tag size is determined as 59 bps INFO @ Tue, 14 Jul 2020 10:54:24: #1 tag size = 59 INFO @ Tue, 14 Jul 2020 10:54:24: #1 total tags in treatment: 3900474 INFO @ Tue, 14 Jul 2020 10:54:24: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:54:24: #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 10:54:24: #1 tags after filtering in treatment: 3900474 INFO @ Tue, 14 Jul 2020 10:54:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:54:24: #1 finished! INFO @ Tue, 14 Jul 2020 10:54:24: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:54:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:54:24: #2 number of paired peaks: 571 WARNING @ Tue, 14 Jul 2020 10:54:24: Fewer paired peaks (571) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 571 pairs to build model! INFO @ Tue, 14 Jul 2020 10:54:24: start model_add_line... INFO @ Tue, 14 Jul 2020 10:54:25: start X-correlation... INFO @ Tue, 14 Jul 2020 10:54:25: end of X-cor INFO @ Tue, 14 Jul 2020 10:54:25: #2 finished! INFO @ Tue, 14 Jul 2020 10:54:25: #2 predicted fragment length is 56 bps INFO @ Tue, 14 Jul 2020 10:54:25: #2 alternative fragment length(s) may be 56 bps INFO @ Tue, 14 Jul 2020 10:54:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521323/SRX8521323.20_model.r WARNING @ Tue, 14 Jul 2020 10:54:25: #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 10:54:25: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Tue, 14 Jul 2020 10:54:25: #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 10:54:25: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:54:25: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 10:54:33: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:54:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521323/SRX8521323.20_peaks.xls INFO @ Tue, 14 Jul 2020 10:54:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521323/SRX8521323.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:54:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521323/SRX8521323.20_summits.bed INFO @ Tue, 14 Jul 2020 10:54:37: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (156 records, 4 fields): 2 millis CompletedMACS2peakCalling