Job ID = 6627274 SRX = SRX8521341 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T01:46:55 prefetch.2.10.7: 1) Downloading 'SRR11978572'... 2020-07-14T01:46:55 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:47:53 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:47:54 prefetch.2.10.7: 'SRR11978572' is valid 2020-07-14T01:47:54 prefetch.2.10.7: 1) 'SRR11978572' was downloaded successfully 2020-07-14T01:47:54 prefetch.2.10.7: 'SRR11978572' has 0 unresolved dependencies Read 9409937 spots for SRR11978572/SRR11978572.sra Written 9409937 spots for SRR11978572/SRR11978572.sra 2020-07-14T01:48:40 prefetch.2.10.7: 1) Downloading 'SRR11978573'... 2020-07-14T01:48:40 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:51:12 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:51:12 prefetch.2.10.7: 'SRR11978573' is valid 2020-07-14T01:51:12 prefetch.2.10.7: 1) 'SRR11978573' was downloaded successfully 2020-07-14T01:51:12 prefetch.2.10.7: 'SRR11978573' has 0 unresolved dependencies Read 9304637 spots for SRR11978573/SRR11978573.sra Written 9304637 spots for SRR11978573/SRR11978573.sra 2020-07-14T01:52:05 prefetch.2.10.7: 1) Downloading 'SRR11978574'... 2020-07-14T01:52:05 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:53:35 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:53:35 prefetch.2.10.7: 'SRR11978574' is valid 2020-07-14T01:53:35 prefetch.2.10.7: 1) 'SRR11978574' was downloaded successfully 2020-07-14T01:53:35 prefetch.2.10.7: 'SRR11978574' has 0 unresolved dependencies Read 9305809 spots for SRR11978574/SRR11978574.sra Written 9305809 spots for SRR11978574/SRR11978574.sra 2020-07-14T01:54:20 prefetch.2.10.7: 1) Downloading 'SRR11978575'... 2020-07-14T01:54:20 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:55:22 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:55:22 prefetch.2.10.7: 'SRR11978575' is valid 2020-07-14T01:55:22 prefetch.2.10.7: 1) 'SRR11978575' was downloaded successfully 2020-07-14T01:55:22 prefetch.2.10.7: 'SRR11978575' has 0 unresolved dependencies Read 9704020 spots for SRR11978575/SRR11978575.sra Written 9704020 spots for SRR11978575/SRR11978575.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627507 ("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: 00:06:56 37724403 reads; of these: 37724403 (100.00%) were unpaired; of these: 29641158 (78.57%) aligned 0 times 5594807 (14.83%) aligned exactly 1 time 2488438 (6.60%) aligned >1 times 21.43% overall alignment rate Time searching: 00:06:56 Overall time: 00:06:56 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] 1475881 / 8083245 = 0.1826 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 11:05:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521341/SRX8521341.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521341/SRX8521341.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521341/SRX8521341.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521341/SRX8521341.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 11:05:36: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:05:36: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:05:42: 1000000 INFO @ Tue, 14 Jul 2020 11:05:47: 2000000 INFO @ Tue, 14 Jul 2020 11:05:52: 3000000 INFO @ Tue, 14 Jul 2020 11:05:58: 4000000 INFO @ Tue, 14 Jul 2020 11:06:03: 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 11:06:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521341/SRX8521341.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521341/SRX8521341.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521341/SRX8521341.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521341/SRX8521341.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 11:06:06: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:06:06: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:06:09: 6000000 INFO @ Tue, 14 Jul 2020 11:06:12: #1 tag size is determined as 62 bps INFO @ Tue, 14 Jul 2020 11:06:12: #1 tag size = 62 INFO @ Tue, 14 Jul 2020 11:06:12: #1 total tags in treatment: 6607364 INFO @ Tue, 14 Jul 2020 11:06:12: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:06:12: #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 11:06:12: #1 tags after filtering in treatment: 6607364 INFO @ Tue, 14 Jul 2020 11:06:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:06:12: #1 finished! INFO @ Tue, 14 Jul 2020 11:06:12: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:06:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:06:13: #2 number of paired peaks: 257 WARNING @ Tue, 14 Jul 2020 11:06:13: Fewer paired peaks (257) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 257 pairs to build model! INFO @ Tue, 14 Jul 2020 11:06:13: start model_add_line... INFO @ Tue, 14 Jul 2020 11:06:13: start X-correlation... INFO @ Tue, 14 Jul 2020 11:06:13: end of X-cor INFO @ Tue, 14 Jul 2020 11:06:13: #2 finished! INFO @ Tue, 14 Jul 2020 11:06:13: #2 predicted fragment length is 56 bps INFO @ Tue, 14 Jul 2020 11:06:13: #2 alternative fragment length(s) may be 56 bps INFO @ Tue, 14 Jul 2020 11:06:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521341/SRX8521341.05_model.r WARNING @ Tue, 14 Jul 2020 11:06:13: #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 11:06:13: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Tue, 14 Jul 2020 11:06:13: #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 11:06:13: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:06:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:06:13: 1000000 INFO @ Tue, 14 Jul 2020 11:06:20: 2000000 INFO @ Tue, 14 Jul 2020 11:06:26: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:06:26: 3000000 INFO @ Tue, 14 Jul 2020 11:06:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521341/SRX8521341.05_peaks.xls INFO @ Tue, 14 Jul 2020 11:06:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521341/SRX8521341.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:06:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521341/SRX8521341.05_summits.bed INFO @ Tue, 14 Jul 2020 11:06:33: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1418 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:06:34: 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 11:06:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521341/SRX8521341.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521341/SRX8521341.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521341/SRX8521341.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521341/SRX8521341.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 11:06:36: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:06:36: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:06:41: 5000000 INFO @ Tue, 14 Jul 2020 11:06:42: 1000000 INFO @ Tue, 14 Jul 2020 11:06:48: 6000000 INFO @ Tue, 14 Jul 2020 11:06:48: 2000000 INFO @ Tue, 14 Jul 2020 11:06:52: #1 tag size is determined as 62 bps INFO @ Tue, 14 Jul 2020 11:06:52: #1 tag size = 62 INFO @ Tue, 14 Jul 2020 11:06:52: #1 total tags in treatment: 6607364 INFO @ Tue, 14 Jul 2020 11:06:52: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:06:52: #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 11:06:52: #1 tags after filtering in treatment: 6607364 INFO @ Tue, 14 Jul 2020 11:06:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:06:52: #1 finished! INFO @ Tue, 14 Jul 2020 11:06:52: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:06:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:06:52: #2 number of paired peaks: 257 WARNING @ Tue, 14 Jul 2020 11:06:52: Fewer paired peaks (257) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 257 pairs to build model! INFO @ Tue, 14 Jul 2020 11:06:52: start model_add_line... INFO @ Tue, 14 Jul 2020 11:06:52: start X-correlation... INFO @ Tue, 14 Jul 2020 11:06:52: end of X-cor INFO @ Tue, 14 Jul 2020 11:06:52: #2 finished! INFO @ Tue, 14 Jul 2020 11:06:52: #2 predicted fragment length is 56 bps INFO @ Tue, 14 Jul 2020 11:06:52: #2 alternative fragment length(s) may be 56 bps INFO @ Tue, 14 Jul 2020 11:06:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521341/SRX8521341.10_model.r WARNING @ Tue, 14 Jul 2020 11:06:52: #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 11:06:52: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Tue, 14 Jul 2020 11:06:52: #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 11:06:52: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:06:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:06:54: 3000000 INFO @ Tue, 14 Jul 2020 11:07:00: 4000000 INFO @ Tue, 14 Jul 2020 11:07:05: 5000000 INFO @ Tue, 14 Jul 2020 11:07:06: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:07:11: 6000000 INFO @ Tue, 14 Jul 2020 11:07:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521341/SRX8521341.10_peaks.xls INFO @ Tue, 14 Jul 2020 11:07:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521341/SRX8521341.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:07:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521341/SRX8521341.10_summits.bed INFO @ Tue, 14 Jul 2020 11:07:13: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (840 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 11:07:14: #1 tag size is determined as 62 bps INFO @ Tue, 14 Jul 2020 11:07:14: #1 tag size = 62 INFO @ Tue, 14 Jul 2020 11:07:14: #1 total tags in treatment: 6607364 INFO @ Tue, 14 Jul 2020 11:07:14: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:07:14: #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 11:07:15: #1 tags after filtering in treatment: 6607364 INFO @ Tue, 14 Jul 2020 11:07:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:07:15: #1 finished! INFO @ Tue, 14 Jul 2020 11:07:15: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:07:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:07:15: #2 number of paired peaks: 257 WARNING @ Tue, 14 Jul 2020 11:07:15: Fewer paired peaks (257) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 257 pairs to build model! INFO @ Tue, 14 Jul 2020 11:07:15: start model_add_line... INFO @ Tue, 14 Jul 2020 11:07:15: start X-correlation... INFO @ Tue, 14 Jul 2020 11:07:15: end of X-cor INFO @ Tue, 14 Jul 2020 11:07:15: #2 finished! INFO @ Tue, 14 Jul 2020 11:07:15: #2 predicted fragment length is 56 bps INFO @ Tue, 14 Jul 2020 11:07:15: #2 alternative fragment length(s) may be 56 bps INFO @ Tue, 14 Jul 2020 11:07:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521341/SRX8521341.20_model.r WARNING @ Tue, 14 Jul 2020 11:07:15: #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 11:07:15: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Tue, 14 Jul 2020 11:07:15: #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 11:07:15: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:07:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:07:29: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 11:07:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521341/SRX8521341.20_peaks.xls INFO @ Tue, 14 Jul 2020 11:07:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521341/SRX8521341.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:07:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521341/SRX8521341.20_summits.bed INFO @ Tue, 14 Jul 2020 11:07:36: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (388 records, 4 fields): 2 millis CompletedMACS2peakCalling