Job ID = 6457019 SRX = SRX4315042 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:29:55 prefetch.2.10.7: 1) Downloading 'SRR7444503'... 2020-06-21T11:29:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:30:47 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:30:48 prefetch.2.10.7: 'SRR7444503' is valid 2020-06-21T11:30:48 prefetch.2.10.7: 1) 'SRR7444503' was downloaded successfully 2020-06-21T11:31:25 prefetch.2.10.7: 'SRR7444503' has 7 unresolved dependencies 2020-06-21T11:31:25 prefetch.2.10.7: 2) Downloading 'ncbi-acc:AE013599.5?vdb-ctx=refseq'... 2020-06-21T11:31:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:31:42 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:31:42 prefetch.2.10.7: 2) 'ncbi-acc:AE013599.5?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:31:42 prefetch.2.10.7: 3) Downloading 'ncbi-acc:AE014134.6?vdb-ctx=refseq'... 2020-06-21T11:31:42 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:31:58 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:31:58 prefetch.2.10.7: 3) 'ncbi-acc:AE014134.6?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:31:58 prefetch.2.10.7: 4) Downloading 'ncbi-acc:AE014135.4?vdb-ctx=refseq'... 2020-06-21T11:31:58 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:32:11 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:32:11 prefetch.2.10.7: 4) 'ncbi-acc:AE014135.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:32:11 prefetch.2.10.7: 5) Downloading 'ncbi-acc:AE014296.5?vdb-ctx=refseq'... 2020-06-21T11:32:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:32:28 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:32:28 prefetch.2.10.7: 5) 'ncbi-acc:AE014296.5?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:32:28 prefetch.2.10.7: 6) Downloading 'ncbi-acc:AE014297.3?vdb-ctx=refseq'... 2020-06-21T11:32:28 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:32:45 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:32:45 prefetch.2.10.7: 6) 'ncbi-acc:AE014297.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:32:45 prefetch.2.10.7: 7) Downloading 'ncbi-acc:AE014298.5?vdb-ctx=refseq'... 2020-06-21T11:32:45 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:33:02 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:33:02 prefetch.2.10.7: 7) 'ncbi-acc:AE014298.5?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:33:02 prefetch.2.10.7: 8) Downloading 'ncbi-acc:CP007106.1?vdb-ctx=refseq'... 2020-06-21T11:33:02 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:33:16 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:33:16 prefetch.2.10.7: 8) 'ncbi-acc:CP007106.1?vdb-ctx=refseq' was downloaded successfully Read 6917936 spots for SRR7444503/SRR7444503.sra Written 6917936 spots for SRR7444503/SRR7444503.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: 00:01:56 6917936 reads; of these: 6917936 (100.00%) were unpaired; of these: 4827 (0.07%) aligned 0 times 6014903 (86.95%) aligned exactly 1 time 898206 (12.98%) aligned >1 times 99.93% overall alignment rate Time searching: 00:01:56 Overall time: 00:01:56 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_rmdupse_core] 3121320 / 6913109 = 0.4515 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 20:37:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4315042/SRX4315042.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4315042/SRX4315042.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4315042/SRX4315042.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4315042/SRX4315042.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 20:37:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:37:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:37:48: 1000000 INFO @ Sun, 21 Jun 2020 20:37:56: 2000000 INFO @ Sun, 21 Jun 2020 20:38:03: 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 20:38:09: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 20:38:09: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 20:38:09: #1 total tags in treatment: 3791789 INFO @ Sun, 21 Jun 2020 20:38:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:38:09: #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 20:38:10: #1 tags after filtering in treatment: 3791524 INFO @ Sun, 21 Jun 2020 20:38:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:38:10: #1 finished! INFO @ Sun, 21 Jun 2020 20:38:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:38:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:38:10: #2 number of paired peaks: 525 WARNING @ Sun, 21 Jun 2020 20:38:10: Fewer paired peaks (525) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 525 pairs to build model! INFO @ Sun, 21 Jun 2020 20:38:10: start model_add_line... INFO @ Sun, 21 Jun 2020 20:38:10: start X-correlation... INFO @ Sun, 21 Jun 2020 20:38:10: end of X-cor INFO @ Sun, 21 Jun 2020 20:38:10: #2 finished! INFO @ Sun, 21 Jun 2020 20:38:10: #2 predicted fragment length is 81 bps INFO @ Sun, 21 Jun 2020 20:38:10: #2 alternative fragment length(s) may be 81 bps INFO @ Sun, 21 Jun 2020 20:38:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4315042/SRX4315042.05_model.r WARNING @ Sun, 21 Jun 2020 20:38:10: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:38:10: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Sun, 21 Jun 2020 20:38:10: #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 20:38:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:38:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:38:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4315042/SRX4315042.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4315042/SRX4315042.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4315042/SRX4315042.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4315042/SRX4315042.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 20:38:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:38:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:38:17: 1000000 INFO @ Sun, 21 Jun 2020 20:38:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:38:23: 2000000 INFO @ Sun, 21 Jun 2020 20:38:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4315042/SRX4315042.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:38:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4315042/SRX4315042.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:38:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4315042/SRX4315042.05_summits.bed INFO @ Sun, 21 Jun 2020 20:38:23: Done! pass1 - making usageList (132 chroms): 1 millis pass2 - checking and writing primary data (970 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:38:29: 3000000 INFO @ Sun, 21 Jun 2020 20:38:34: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 20:38:34: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 20:38:34: #1 total tags in treatment: 3791789 INFO @ Sun, 21 Jun 2020 20:38:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:38:34: #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 20:38:34: #1 tags after filtering in treatment: 3791524 INFO @ Sun, 21 Jun 2020 20:38:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:38:34: #1 finished! INFO @ Sun, 21 Jun 2020 20:38:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:38:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:38:35: #2 number of paired peaks: 525 WARNING @ Sun, 21 Jun 2020 20:38:35: Fewer paired peaks (525) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 525 pairs to build model! INFO @ Sun, 21 Jun 2020 20:38:35: start model_add_line... INFO @ Sun, 21 Jun 2020 20:38:35: start X-correlation... INFO @ Sun, 21 Jun 2020 20:38:35: end of X-cor INFO @ Sun, 21 Jun 2020 20:38:35: #2 finished! INFO @ Sun, 21 Jun 2020 20:38:35: #2 predicted fragment length is 81 bps INFO @ Sun, 21 Jun 2020 20:38:35: #2 alternative fragment length(s) may be 81 bps INFO @ Sun, 21 Jun 2020 20:38:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4315042/SRX4315042.10_model.r WARNING @ Sun, 21 Jun 2020 20:38:35: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:38:35: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Sun, 21 Jun 2020 20:38:35: #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 20:38:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:38:35: #3 Pre-compute pvalue-qvalue table... 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 20:38:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4315042/SRX4315042.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4315042/SRX4315042.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4315042/SRX4315042.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4315042/SRX4315042.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 20:38:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:38:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:38:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:38:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4315042/SRX4315042.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:38:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4315042/SRX4315042.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:38:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4315042/SRX4315042.10_summits.bed INFO @ Sun, 21 Jun 2020 20:38:48: Done! INFO @ Sun, 21 Jun 2020 20:38:48: 1000000 pass1 - making usageList (97 chroms): 1 millis pass2 - checking and writing primary data (372 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:38:55: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:39:03: 3000000 INFO @ Sun, 21 Jun 2020 20:39:09: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 20:39:09: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 20:39:09: #1 total tags in treatment: 3791789 INFO @ Sun, 21 Jun 2020 20:39:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:39:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:39:09: #1 tags after filtering in treatment: 3791524 INFO @ Sun, 21 Jun 2020 20:39:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:39:09: #1 finished! INFO @ Sun, 21 Jun 2020 20:39:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:39:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:39:09: #2 number of paired peaks: 525 WARNING @ Sun, 21 Jun 2020 20:39:09: Fewer paired peaks (525) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 525 pairs to build model! INFO @ Sun, 21 Jun 2020 20:39:09: start model_add_line... INFO @ Sun, 21 Jun 2020 20:39:09: start X-correlation... INFO @ Sun, 21 Jun 2020 20:39:09: end of X-cor INFO @ Sun, 21 Jun 2020 20:39:09: #2 finished! INFO @ Sun, 21 Jun 2020 20:39:09: #2 predicted fragment length is 81 bps INFO @ Sun, 21 Jun 2020 20:39:09: #2 alternative fragment length(s) may be 81 bps INFO @ Sun, 21 Jun 2020 20:39:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4315042/SRX4315042.20_model.r WARNING @ Sun, 21 Jun 2020 20:39:09: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:39:09: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Sun, 21 Jun 2020 20:39:09: #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 20:39:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:39:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:39:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:39:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4315042/SRX4315042.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:39:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4315042/SRX4315042.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:39:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4315042/SRX4315042.20_summits.bed INFO @ Sun, 21 Jun 2020 20:39:22: Done! pass1 - making usageList (63 chroms): 1 millis pass2 - checking and writing primary data (136 records, 4 fields): 3 millis CompletedMACS2peakCalling