Job ID = 6627303 SRX = SRX8521363 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T01:55:25 prefetch.2.10.7: 1) Downloading 'SRR11978118'... 2020-07-14T01:55:25 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:56:35 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:56:35 prefetch.2.10.7: 'SRR11978118' is valid 2020-07-14T01:56:35 prefetch.2.10.7: 1) 'SRR11978118' was downloaded successfully 2020-07-14T01:56:35 prefetch.2.10.7: 'SRR11978118' has 0 unresolved dependencies Read 8971359 spots for SRR11978118/SRR11978118.sra Written 8971359 spots for SRR11978118/SRR11978118.sra 2020-07-14T01:57:20 prefetch.2.10.7: 1) Downloading 'SRR11978119'... 2020-07-14T01:57:20 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:58:41 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:58:42 prefetch.2.10.7: 'SRR11978119' is valid 2020-07-14T01:58:42 prefetch.2.10.7: 1) 'SRR11978119' was downloaded successfully 2020-07-14T01:58:42 prefetch.2.10.7: 'SRR11978119' has 0 unresolved dependencies Read 8863991 spots for SRR11978119/SRR11978119.sra Written 8863991 spots for SRR11978119/SRR11978119.sra 2020-07-14T01:59:26 prefetch.2.10.7: 1) Downloading 'SRR11978120'... 2020-07-14T01:59:26 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:02:07 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:02:07 prefetch.2.10.7: 'SRR11978120' is valid 2020-07-14T02:02:07 prefetch.2.10.7: 1) 'SRR11978120' was downloaded successfully 2020-07-14T02:02:07 prefetch.2.10.7: 'SRR11978120' has 0 unresolved dependencies Read 9089860 spots for SRR11978120/SRR11978120.sra Written 9089860 spots for SRR11978120/SRR11978120.sra 2020-07-14T02:02:54 prefetch.2.10.7: 1) Downloading 'SRR11978121'... 2020-07-14T02:02:54 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:05:31 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:05:31 prefetch.2.10.7: 'SRR11978121' is valid 2020-07-14T02:05:31 prefetch.2.10.7: 1) 'SRR11978121' was downloaded successfully 2020-07-14T02:05:31 prefetch.2.10.7: 'SRR11978121' has 0 unresolved dependencies Read 8922272 spots for SRR11978121/SRR11978121.sra Written 8922272 spots for SRR11978121/SRR11978121.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627528 ("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: 00:06:03 35847482 reads; of these: 35847482 (100.00%) were unpaired; of these: 29448447 (82.15%) aligned 0 times 4586623 (12.79%) aligned exactly 1 time 1812412 (5.06%) aligned >1 times 17.85% overall alignment rate Time searching: 00:06:03 Overall time: 00:06:03 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] 1088229 / 6399035 = 0.1701 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 11:14:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521363/SRX8521363.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521363/SRX8521363.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521363/SRX8521363.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521363/SRX8521363.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 11:14:39: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:14:39: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:14:45: 1000000 INFO @ Tue, 14 Jul 2020 11:14:51: 2000000 INFO @ Tue, 14 Jul 2020 11:14:58: 3000000 INFO @ Tue, 14 Jul 2020 11:15:05: 4000000 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 11:15:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521363/SRX8521363.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521363/SRX8521363.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521363/SRX8521363.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521363/SRX8521363.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 11:15:09: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:15:09: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:15:12: 5000000 INFO @ Tue, 14 Jul 2020 11:15:14: #1 tag size is determined as 70 bps INFO @ Tue, 14 Jul 2020 11:15:14: #1 tag size = 70 INFO @ Tue, 14 Jul 2020 11:15:14: #1 total tags in treatment: 5310806 INFO @ Tue, 14 Jul 2020 11:15:14: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:15:14: #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 11:15:15: #1 tags after filtering in treatment: 5310806 INFO @ Tue, 14 Jul 2020 11:15:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:15:15: #1 finished! INFO @ Tue, 14 Jul 2020 11:15:15: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:15:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:15:15: #2 number of paired peaks: 329 WARNING @ Tue, 14 Jul 2020 11:15:15: Fewer paired peaks (329) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 329 pairs to build model! INFO @ Tue, 14 Jul 2020 11:15:15: start model_add_line... INFO @ Tue, 14 Jul 2020 11:15:15: start X-correlation... INFO @ Tue, 14 Jul 2020 11:15:15: end of X-cor INFO @ Tue, 14 Jul 2020 11:15:15: #2 finished! INFO @ Tue, 14 Jul 2020 11:15:15: #2 predicted fragment length is 61 bps INFO @ Tue, 14 Jul 2020 11:15:15: #2 alternative fragment length(s) may be 61 bps INFO @ Tue, 14 Jul 2020 11:15:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521363/SRX8521363.05_model.r WARNING @ Tue, 14 Jul 2020 11:15:15: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:15:15: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Tue, 14 Jul 2020 11:15:15: #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 11:15:15: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:15:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:15:16: 1000000 INFO @ Tue, 14 Jul 2020 11:15:23: 2000000 INFO @ Tue, 14 Jul 2020 11:15:27: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:15:29: 3000000 INFO @ Tue, 14 Jul 2020 11:15:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521363/SRX8521363.05_peaks.xls INFO @ Tue, 14 Jul 2020 11:15:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521363/SRX8521363.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:15:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521363/SRX8521363.05_summits.bed INFO @ Tue, 14 Jul 2020 11:15:33: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1543 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:15:36: 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 11:15:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521363/SRX8521363.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521363/SRX8521363.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521363/SRX8521363.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521363/SRX8521363.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 11:15:39: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:15:39: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:15:43: 5000000 INFO @ Tue, 14 Jul 2020 11:15:45: #1 tag size is determined as 70 bps INFO @ Tue, 14 Jul 2020 11:15:45: #1 tag size = 70 INFO @ Tue, 14 Jul 2020 11:15:45: #1 total tags in treatment: 5310806 INFO @ Tue, 14 Jul 2020 11:15:45: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:15:45: #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 11:15:45: #1 tags after filtering in treatment: 5310806 INFO @ Tue, 14 Jul 2020 11:15:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:15:45: #1 finished! INFO @ Tue, 14 Jul 2020 11:15:45: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:15:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:15:45: #2 number of paired peaks: 329 WARNING @ Tue, 14 Jul 2020 11:15:45: Fewer paired peaks (329) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 329 pairs to build model! INFO @ Tue, 14 Jul 2020 11:15:45: start model_add_line... INFO @ Tue, 14 Jul 2020 11:15:45: start X-correlation... INFO @ Tue, 14 Jul 2020 11:15:45: end of X-cor INFO @ Tue, 14 Jul 2020 11:15:45: #2 finished! INFO @ Tue, 14 Jul 2020 11:15:45: #2 predicted fragment length is 61 bps INFO @ Tue, 14 Jul 2020 11:15:45: #2 alternative fragment length(s) may be 61 bps INFO @ Tue, 14 Jul 2020 11:15:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521363/SRX8521363.10_model.r WARNING @ Tue, 14 Jul 2020 11:15:45: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:15:45: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Tue, 14 Jul 2020 11:15:45: #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 11:15:45: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:15:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:15:46: 1000000 INFO @ Tue, 14 Jul 2020 11:15:54: 2000000 INFO @ Tue, 14 Jul 2020 11:15:58: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:16:01: 3000000 INFO @ Tue, 14 Jul 2020 11:16:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521363/SRX8521363.10_peaks.xls INFO @ Tue, 14 Jul 2020 11:16:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521363/SRX8521363.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:16:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521363/SRX8521363.10_summits.bed INFO @ Tue, 14 Jul 2020 11:16:04: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (619 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 11:16:08: 4000000 INFO @ Tue, 14 Jul 2020 11:16:15: 5000000 INFO @ Tue, 14 Jul 2020 11:16:17: #1 tag size is determined as 70 bps INFO @ Tue, 14 Jul 2020 11:16:17: #1 tag size = 70 INFO @ Tue, 14 Jul 2020 11:16:17: #1 total tags in treatment: 5310806 INFO @ Tue, 14 Jul 2020 11:16:17: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:16:17: #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 11:16:17: #1 tags after filtering in treatment: 5310806 INFO @ Tue, 14 Jul 2020 11:16:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:16:17: #1 finished! INFO @ Tue, 14 Jul 2020 11:16:17: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:16:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:16:18: #2 number of paired peaks: 329 WARNING @ Tue, 14 Jul 2020 11:16:18: Fewer paired peaks (329) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 329 pairs to build model! INFO @ Tue, 14 Jul 2020 11:16:18: start model_add_line... INFO @ Tue, 14 Jul 2020 11:16:18: start X-correlation... INFO @ Tue, 14 Jul 2020 11:16:18: end of X-cor INFO @ Tue, 14 Jul 2020 11:16:18: #2 finished! INFO @ Tue, 14 Jul 2020 11:16:18: #2 predicted fragment length is 61 bps INFO @ Tue, 14 Jul 2020 11:16:18: #2 alternative fragment length(s) may be 61 bps INFO @ Tue, 14 Jul 2020 11:16:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521363/SRX8521363.20_model.r WARNING @ Tue, 14 Jul 2020 11:16:18: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:16:18: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Tue, 14 Jul 2020 11:16:18: #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 11:16:18: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:16:18: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 11:16:29: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:16:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521363/SRX8521363.20_peaks.xls INFO @ Tue, 14 Jul 2020 11:16:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521363/SRX8521363.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:16:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521363/SRX8521363.20_summits.bed INFO @ Tue, 14 Jul 2020 11:16:35: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (127 records, 4 fields): 2 millis CompletedMACS2peakCalling