Job ID = 6627453 SRX = SRX8521385 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T02:34:47 prefetch.2.10.7: 1) Downloading 'SRR11978282'... 2020-07-14T02:34:47 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:36:11 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:36:12 prefetch.2.10.7: 'SRR11978282' is valid 2020-07-14T02:36:12 prefetch.2.10.7: 1) 'SRR11978282' was downloaded successfully 2020-07-14T02:36:12 prefetch.2.10.7: 'SRR11978282' has 0 unresolved dependencies Read 12842828 spots for SRR11978282/SRR11978282.sra Written 12842828 spots for SRR11978282/SRR11978282.sra 2020-07-14T02:37:08 prefetch.2.10.7: 1) Downloading 'SRR11978283'... 2020-07-14T02:37:08 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:38:11 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:38:11 prefetch.2.10.7: 'SRR11978283' is valid 2020-07-14T02:38:11 prefetch.2.10.7: 1) 'SRR11978283' was downloaded successfully 2020-07-14T02:38:11 prefetch.2.10.7: 'SRR11978283' has 0 unresolved dependencies Read 12697575 spots for SRR11978283/SRR11978283.sra Written 12697575 spots for SRR11978283/SRR11978283.sra 2020-07-14T02:39:09 prefetch.2.10.7: 1) Downloading 'SRR11978284'... 2020-07-14T02:39:09 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:40:38 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:40:38 prefetch.2.10.7: 'SRR11978284' is valid 2020-07-14T02:40:38 prefetch.2.10.7: 1) 'SRR11978284' was downloaded successfully 2020-07-14T02:40:38 prefetch.2.10.7: 'SRR11978284' has 0 unresolved dependencies Read 12665228 spots for SRR11978284/SRR11978284.sra Written 12665228 spots for SRR11978284/SRR11978284.sra 2020-07-14T02:41:34 prefetch.2.10.7: 1) Downloading 'SRR11978285'... 2020-07-14T02:41:34 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:42:32 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:42:33 prefetch.2.10.7: 'SRR11978285' is valid 2020-07-14T02:42:33 prefetch.2.10.7: 1) 'SRR11978285' was downloaded successfully 2020-07-14T02:42:33 prefetch.2.10.7: 'SRR11978285' has 0 unresolved dependencies Read 12768506 spots for SRR11978285/SRR11978285.sra Written 12768506 spots for SRR11978285/SRR11978285.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627648 ("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: 00:07:20 50974137 reads; of these: 50974137 (100.00%) were unpaired; of these: 46363781 (90.96%) aligned 0 times 3404974 (6.68%) aligned exactly 1 time 1205382 (2.36%) aligned >1 times 9.04% overall alignment rate Time searching: 00:07:20 Overall time: 00:07:20 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] 921352 / 4610356 = 0.1998 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 11:52:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521385/SRX8521385.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521385/SRX8521385.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521385/SRX8521385.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521385/SRX8521385.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 11:52:33: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:52:33: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:52:38: 1000000 INFO @ Tue, 14 Jul 2020 11:52:43: 2000000 INFO @ Tue, 14 Jul 2020 11:52:48: 3000000 INFO @ Tue, 14 Jul 2020 11:52:51: #1 tag size is determined as 55 bps INFO @ Tue, 14 Jul 2020 11:52:51: #1 tag size = 55 INFO @ Tue, 14 Jul 2020 11:52:51: #1 total tags in treatment: 3689004 INFO @ Tue, 14 Jul 2020 11:52:51: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:52:51: #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 11:52:51: #1 tags after filtering in treatment: 3689004 INFO @ Tue, 14 Jul 2020 11:52:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:52:51: #1 finished! INFO @ Tue, 14 Jul 2020 11:52:51: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:52:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:52:52: #2 number of paired peaks: 631 WARNING @ Tue, 14 Jul 2020 11:52:52: Fewer paired peaks (631) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 631 pairs to build model! INFO @ Tue, 14 Jul 2020 11:52:52: start model_add_line... INFO @ Tue, 14 Jul 2020 11:52:52: start X-correlation... INFO @ Tue, 14 Jul 2020 11:52:52: end of X-cor INFO @ Tue, 14 Jul 2020 11:52:52: #2 finished! INFO @ Tue, 14 Jul 2020 11:52:52: #2 predicted fragment length is 62 bps INFO @ Tue, 14 Jul 2020 11:52:52: #2 alternative fragment length(s) may be 62 bps INFO @ Tue, 14 Jul 2020 11:52:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521385/SRX8521385.05_model.r WARNING @ Tue, 14 Jul 2020 11:52:52: #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 11:52:52: #2 You may need to consider one of the other alternative d(s): 62 WARNING @ Tue, 14 Jul 2020 11:52:52: #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 11:52:52: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:52:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:52:59: #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 11:53:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521385/SRX8521385.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521385/SRX8521385.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521385/SRX8521385.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521385/SRX8521385.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 11:53:03: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:53:03: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:53:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521385/SRX8521385.05_peaks.xls INFO @ Tue, 14 Jul 2020 11:53:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521385/SRX8521385.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:53:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521385/SRX8521385.05_summits.bed INFO @ Tue, 14 Jul 2020 11:53:03: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1631 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:53:08: 1000000 INFO @ Tue, 14 Jul 2020 11:53:13: 2000000 INFO @ Tue, 14 Jul 2020 11:53:18: 3000000 INFO @ Tue, 14 Jul 2020 11:53:21: #1 tag size is determined as 55 bps INFO @ Tue, 14 Jul 2020 11:53:21: #1 tag size = 55 INFO @ Tue, 14 Jul 2020 11:53:21: #1 total tags in treatment: 3689004 INFO @ Tue, 14 Jul 2020 11:53:21: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:53:21: #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 11:53:21: #1 tags after filtering in treatment: 3689004 INFO @ Tue, 14 Jul 2020 11:53:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:53:21: #1 finished! INFO @ Tue, 14 Jul 2020 11:53:21: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:53:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:53:22: #2 number of paired peaks: 631 WARNING @ Tue, 14 Jul 2020 11:53:22: Fewer paired peaks (631) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 631 pairs to build model! INFO @ Tue, 14 Jul 2020 11:53:22: start model_add_line... INFO @ Tue, 14 Jul 2020 11:53:22: start X-correlation... INFO @ Tue, 14 Jul 2020 11:53:22: end of X-cor INFO @ Tue, 14 Jul 2020 11:53:22: #2 finished! INFO @ Tue, 14 Jul 2020 11:53:22: #2 predicted fragment length is 62 bps INFO @ Tue, 14 Jul 2020 11:53:22: #2 alternative fragment length(s) may be 62 bps INFO @ Tue, 14 Jul 2020 11:53:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521385/SRX8521385.10_model.r WARNING @ Tue, 14 Jul 2020 11:53:22: #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 11:53:22: #2 You may need to consider one of the other alternative d(s): 62 WARNING @ Tue, 14 Jul 2020 11:53:22: #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 11:53:22: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:53:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:53:30: #3 Call peaks for each chromosome... 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 11:53:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521385/SRX8521385.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521385/SRX8521385.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521385/SRX8521385.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521385/SRX8521385.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 11:53:33: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:53:33: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:53:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521385/SRX8521385.10_peaks.xls INFO @ Tue, 14 Jul 2020 11:53:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521385/SRX8521385.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:53:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521385/SRX8521385.10_summits.bed INFO @ Tue, 14 Jul 2020 11:53:33: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (728 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:53:39: 1000000 INFO @ Tue, 14 Jul 2020 11:53:45: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 11:53:51: 3000000 INFO @ Tue, 14 Jul 2020 11:53:55: #1 tag size is determined as 55 bps INFO @ Tue, 14 Jul 2020 11:53:55: #1 tag size = 55 INFO @ Tue, 14 Jul 2020 11:53:55: #1 total tags in treatment: 3689004 INFO @ Tue, 14 Jul 2020 11:53:55: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:53:55: #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 11:53:55: #1 tags after filtering in treatment: 3689004 INFO @ Tue, 14 Jul 2020 11:53:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:53:55: #1 finished! INFO @ Tue, 14 Jul 2020 11:53:55: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:53:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:53:55: #2 number of paired peaks: 631 WARNING @ Tue, 14 Jul 2020 11:53:55: Fewer paired peaks (631) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 631 pairs to build model! INFO @ Tue, 14 Jul 2020 11:53:55: start model_add_line... INFO @ Tue, 14 Jul 2020 11:53:55: start X-correlation... INFO @ Tue, 14 Jul 2020 11:53:55: end of X-cor INFO @ Tue, 14 Jul 2020 11:53:55: #2 finished! INFO @ Tue, 14 Jul 2020 11:53:55: #2 predicted fragment length is 62 bps INFO @ Tue, 14 Jul 2020 11:53:55: #2 alternative fragment length(s) may be 62 bps INFO @ Tue, 14 Jul 2020 11:53:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521385/SRX8521385.20_model.r WARNING @ Tue, 14 Jul 2020 11:53:55: #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 11:53:55: #2 You may need to consider one of the other alternative d(s): 62 WARNING @ Tue, 14 Jul 2020 11:53:55: #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 11:53:55: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:53:55: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 11:54:03: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:54:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521385/SRX8521385.20_peaks.xls INFO @ Tue, 14 Jul 2020 11:54:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521385/SRX8521385.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:54:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521385/SRX8521385.20_summits.bed INFO @ Tue, 14 Jul 2020 11:54:07: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (182 records, 4 fields): 1 millis CompletedMACS2peakCalling