Job ID = 6457030 SRX = SRX4315052 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:33:55 prefetch.2.10.7: 1) Downloading 'SRR7444513'... 2020-06-21T11:33:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:34:47 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:34:47 prefetch.2.10.7: 'SRR7444513' is valid 2020-06-21T11:34:47 prefetch.2.10.7: 1) 'SRR7444513' was downloaded successfully 2020-06-21T11:35:24 prefetch.2.10.7: 'SRR7444513' has 7 unresolved dependencies 2020-06-21T11:35:24 prefetch.2.10.7: 2) Downloading 'ncbi-acc:AE013599.5?vdb-ctx=refseq'... 2020-06-21T11:35:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:35:42 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:35:42 prefetch.2.10.7: 2) 'ncbi-acc:AE013599.5?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:35:42 prefetch.2.10.7: 3) Downloading 'ncbi-acc:AE014134.6?vdb-ctx=refseq'... 2020-06-21T11:35:42 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:35:59 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:35:59 prefetch.2.10.7: 3) 'ncbi-acc:AE014134.6?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:35:59 prefetch.2.10.7: 4) Downloading 'ncbi-acc:AE014135.4?vdb-ctx=refseq'... 2020-06-21T11:35:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:36:11 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:36:11 prefetch.2.10.7: 4) 'ncbi-acc:AE014135.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:36:11 prefetch.2.10.7: 5) Downloading 'ncbi-acc:AE014296.5?vdb-ctx=refseq'... 2020-06-21T11:36:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:36:30 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:36:30 prefetch.2.10.7: 5) 'ncbi-acc:AE014296.5?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:36:30 prefetch.2.10.7: 6) Downloading 'ncbi-acc:AE014297.3?vdb-ctx=refseq'... 2020-06-21T11:36:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:36:48 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:36:48 prefetch.2.10.7: 6) 'ncbi-acc:AE014297.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:36:48 prefetch.2.10.7: 7) Downloading 'ncbi-acc:AE014298.5?vdb-ctx=refseq'... 2020-06-21T11:36:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:37:08 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:37:08 prefetch.2.10.7: 7) 'ncbi-acc:AE014298.5?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:37:08 prefetch.2.10.7: 8) Downloading 'ncbi-acc:CP007106.1?vdb-ctx=refseq'... 2020-06-21T11:37:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:37:21 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:37:21 prefetch.2.10.7: 8) 'ncbi-acc:CP007106.1?vdb-ctx=refseq' was downloaded successfully Read 9594330 spots for SRR7444513/SRR7444513.sra Written 9594330 spots for SRR7444513/SRR7444513.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:01 9594330 reads; of these: 9594330 (100.00%) were unpaired; of these: 5149 (0.05%) aligned 0 times 8394640 (87.50%) aligned exactly 1 time 1194541 (12.45%) aligned >1 times 99.95% overall alignment rate Time searching: 00:03:01 Overall time: 00:03:01 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_rmdupse_core] 2325098 / 9589181 = 0.2425 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 @ Sun, 21 Jun 2020 20:44:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4315052/SRX4315052.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4315052/SRX4315052.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4315052/SRX4315052.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4315052/SRX4315052.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 @ Sun, 21 Jun 2020 20:44:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:44:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:44:47: 1000000 INFO @ Sun, 21 Jun 2020 20:44:54: 2000000 INFO @ Sun, 21 Jun 2020 20:45:01: 3000000 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 @ Sun, 21 Jun 2020 20:45:09: 4000000 INFO @ Sun, 21 Jun 2020 20:45:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4315052/SRX4315052.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4315052/SRX4315052.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4315052/SRX4315052.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4315052/SRX4315052.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 @ Sun, 21 Jun 2020 20:45:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:45:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:45:17: 5000000 INFO @ Sun, 21 Jun 2020 20:45:17: 1000000 INFO @ Sun, 21 Jun 2020 20:45:26: 2000000 INFO @ Sun, 21 Jun 2020 20:45:26: 6000000 INFO @ Sun, 21 Jun 2020 20:45:34: 3000000 INFO @ Sun, 21 Jun 2020 20:45:34: 7000000 INFO @ Sun, 21 Jun 2020 20:45:36: #1 tag size is determined as 74 bps INFO @ Sun, 21 Jun 2020 20:45:36: #1 tag size = 74 INFO @ Sun, 21 Jun 2020 20:45:36: #1 total tags in treatment: 7264083 INFO @ Sun, 21 Jun 2020 20:45:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:45:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 20:45:37: #1 tags after filtering in treatment: 7263862 INFO @ Sun, 21 Jun 2020 20:45:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:45:37: #1 finished! INFO @ Sun, 21 Jun 2020 20:45:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:45:37: #2 looking for paired plus/minus strand peaks... 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 @ Sun, 21 Jun 2020 20:45:37: #2 number of paired peaks: 269 WARNING @ Sun, 21 Jun 2020 20:45:37: Fewer paired peaks (269) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 269 pairs to build model! INFO @ Sun, 21 Jun 2020 20:45:37: start model_add_line... INFO @ Sun, 21 Jun 2020 20:45:37: start X-correlation... INFO @ Sun, 21 Jun 2020 20:45:37: end of X-cor INFO @ Sun, 21 Jun 2020 20:45:37: #2 finished! INFO @ Sun, 21 Jun 2020 20:45:37: #2 predicted fragment length is 83 bps INFO @ Sun, 21 Jun 2020 20:45:37: #2 alternative fragment length(s) may be 83 bps INFO @ Sun, 21 Jun 2020 20:45:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4315052/SRX4315052.05_model.r WARNING @ Sun, 21 Jun 2020 20:45:37: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:45:37: #2 You may need to consider one of the other alternative d(s): 83 WARNING @ Sun, 21 Jun 2020 20:45:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 20:45:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:45:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:45:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4315052/SRX4315052.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4315052/SRX4315052.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4315052/SRX4315052.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4315052/SRX4315052.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 @ Sun, 21 Jun 2020 20:45:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:45:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:45:41: 4000000 INFO @ Sun, 21 Jun 2020 20:45:48: 1000000 INFO @ Sun, 21 Jun 2020 20:45:50: 5000000 INFO @ Sun, 21 Jun 2020 20:45:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:45:56: 2000000 INFO @ Sun, 21 Jun 2020 20:45:59: 6000000 INFO @ Sun, 21 Jun 2020 20:46:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4315052/SRX4315052.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:46:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4315052/SRX4315052.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:46:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4315052/SRX4315052.05_summits.bed INFO @ Sun, 21 Jun 2020 20:46:00: Done! pass1 - making usageList (127 chroms): 1 millis pass2 - checking and writing primary data (521 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:46:04: 3000000 INFO @ Sun, 21 Jun 2020 20:46:07: 7000000 INFO @ Sun, 21 Jun 2020 20:46:09: #1 tag size is determined as 74 bps INFO @ Sun, 21 Jun 2020 20:46:09: #1 tag size = 74 INFO @ Sun, 21 Jun 2020 20:46:09: #1 total tags in treatment: 7264083 INFO @ Sun, 21 Jun 2020 20:46:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:46:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 20:46:10: #1 tags after filtering in treatment: 7263862 INFO @ Sun, 21 Jun 2020 20:46:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:46:10: #1 finished! INFO @ Sun, 21 Jun 2020 20:46:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:46:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:46:11: #2 number of paired peaks: 269 WARNING @ Sun, 21 Jun 2020 20:46:11: Fewer paired peaks (269) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 269 pairs to build model! INFO @ Sun, 21 Jun 2020 20:46:11: start model_add_line... INFO @ Sun, 21 Jun 2020 20:46:11: start X-correlation... INFO @ Sun, 21 Jun 2020 20:46:11: end of X-cor INFO @ Sun, 21 Jun 2020 20:46:11: #2 finished! INFO @ Sun, 21 Jun 2020 20:46:11: #2 predicted fragment length is 83 bps INFO @ Sun, 21 Jun 2020 20:46:11: #2 alternative fragment length(s) may be 83 bps INFO @ Sun, 21 Jun 2020 20:46:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4315052/SRX4315052.10_model.r WARNING @ Sun, 21 Jun 2020 20:46:11: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:46:11: #2 You may need to consider one of the other alternative d(s): 83 WARNING @ Sun, 21 Jun 2020 20:46:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 20:46:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:46:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:46:12: 4000000 INFO @ Sun, 21 Jun 2020 20:46:21: 5000000 INFO @ Sun, 21 Jun 2020 20:46:25: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:46:30: 6000000 INFO @ Sun, 21 Jun 2020 20:46:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4315052/SRX4315052.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:46:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4315052/SRX4315052.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:46:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4315052/SRX4315052.10_summits.bed INFO @ Sun, 21 Jun 2020 20:46:33: Done! pass1 - making usageList (89 chroms): 1 millis pass2 - checking and writing primary data (244 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:46:38: 7000000 INFO @ Sun, 21 Jun 2020 20:46:40: #1 tag size is determined as 74 bps INFO @ Sun, 21 Jun 2020 20:46:40: #1 tag size = 74 INFO @ Sun, 21 Jun 2020 20:46:40: #1 total tags in treatment: 7264083 INFO @ Sun, 21 Jun 2020 20:46:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:46:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 20:46:41: #1 tags after filtering in treatment: 7263862 INFO @ Sun, 21 Jun 2020 20:46:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:46:41: #1 finished! INFO @ Sun, 21 Jun 2020 20:46:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:46:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:46:41: #2 number of paired peaks: 269 WARNING @ Sun, 21 Jun 2020 20:46:41: Fewer paired peaks (269) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 269 pairs to build model! INFO @ Sun, 21 Jun 2020 20:46:41: start model_add_line... INFO @ Sun, 21 Jun 2020 20:46:41: start X-correlation... INFO @ Sun, 21 Jun 2020 20:46:41: end of X-cor INFO @ Sun, 21 Jun 2020 20:46:41: #2 finished! INFO @ Sun, 21 Jun 2020 20:46:41: #2 predicted fragment length is 83 bps INFO @ Sun, 21 Jun 2020 20:46:41: #2 alternative fragment length(s) may be 83 bps INFO @ Sun, 21 Jun 2020 20:46:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4315052/SRX4315052.20_model.r WARNING @ Sun, 21 Jun 2020 20:46:41: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:46:41: #2 You may need to consider one of the other alternative d(s): 83 WARNING @ Sun, 21 Jun 2020 20:46:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 20:46:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:46:41: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:46:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:47:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4315052/SRX4315052.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:47:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4315052/SRX4315052.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:47:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4315052/SRX4315052.20_summits.bed INFO @ Sun, 21 Jun 2020 20:47:04: Done! pass1 - making usageList (63 chroms): 1 millis pass2 - checking and writing primary data (132 records, 4 fields): 5 millis CompletedMACS2peakCalling