Job ID = 6457714 SRX = SRX474523 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:48:18 prefetch.2.10.7: 1) Downloading 'SRR1174370'... 2020-06-21T11:48:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:49:15 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:49:16 prefetch.2.10.7: 'SRR1174370' is valid 2020-06-21T11:49:16 prefetch.2.10.7: 1) 'SRR1174370' was downloaded successfully 2020-06-21T11:50:07 prefetch.2.10.7: 'SRR1174370' has 10 unresolved dependencies 2020-06-21T11:50:07 prefetch.2.10.7: 2) Downloading 'ncbi-acc:AE013599.4?vdb-ctx=refseq'... 2020-06-21T11:50:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:50:26 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:50:26 prefetch.2.10.7: 2) 'ncbi-acc:AE013599.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:50:26 prefetch.2.10.7: 3) Downloading 'ncbi-acc:AE014134.5?vdb-ctx=refseq'... 2020-06-21T11:50:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:50:45 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:50:45 prefetch.2.10.7: 3) 'ncbi-acc:AE014134.5?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:50:45 prefetch.2.10.7: 4) Downloading 'ncbi-acc:AE014135.3?vdb-ctx=refseq'... 2020-06-21T11:50:45 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:50:57 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:50:57 prefetch.2.10.7: 4) 'ncbi-acc:AE014135.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:50:57 prefetch.2.10.7: 5) Downloading 'ncbi-acc:AE014296.4?vdb-ctx=refseq'... 2020-06-21T11:50:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:51:19 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:51:19 prefetch.2.10.7: 5) 'ncbi-acc:AE014296.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:51:19 prefetch.2.10.7: 6) Downloading 'ncbi-acc:AE014297.2?vdb-ctx=refseq'... 2020-06-21T11:51:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:51:39 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:51:39 prefetch.2.10.7: 6) 'ncbi-acc:AE014297.2?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:51:39 prefetch.2.10.7: 7) Downloading 'ncbi-acc:AE014298.4?vdb-ctx=refseq'... 2020-06-21T11:51:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:51:55 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:51:55 prefetch.2.10.7: 7) 'ncbi-acc:AE014298.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:51:55 prefetch.2.10.7: 8) Downloading 'ncbi-acc:CM000457.1?vdb-ctx=refseq'... 2020-06-21T11:51:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:52:09 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:52:09 prefetch.2.10.7: 8) 'ncbi-acc:CM000457.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:52:09 prefetch.2.10.7: 9) Downloading 'ncbi-acc:CM000458.1?vdb-ctx=refseq'... 2020-06-21T11:52:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:52:23 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:52:23 prefetch.2.10.7: 9) 'ncbi-acc:CM000458.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:52:23 prefetch.2.10.7: 10) Downloading 'ncbi-acc:CM000459.1?vdb-ctx=refseq'... 2020-06-21T11:52:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:52:37 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:52:37 prefetch.2.10.7: 10) 'ncbi-acc:CM000459.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:52:37 prefetch.2.10.7: 11) Downloading 'ncbi-acc:FA000001.1?vdb-ctx=refseq'... 2020-06-21T11:52:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:52:52 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:52:52 prefetch.2.10.7: 11) 'ncbi-acc:FA000001.1?vdb-ctx=refseq' was downloaded successfully Read 9517831 spots for SRR1174370/SRR1174370.sra Written 9517831 spots for SRR1174370/SRR1174370.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: 00:02:31 9517831 reads; of these: 9517831 (100.00%) were unpaired; of these: 196391 (2.06%) aligned 0 times 6460051 (67.87%) aligned exactly 1 time 2861389 (30.06%) aligned >1 times 97.94% overall alignment rate Time searching: 00:02:31 Overall time: 00:02:31 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] 552348 / 9321440 = 0.0593 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 20:58:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX474523/SRX474523.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX474523/SRX474523.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX474523/SRX474523.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX474523/SRX474523.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 20:58:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:58:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:58:52: 1000000 INFO @ Sun, 21 Jun 2020 20:58:57: 2000000 INFO @ Sun, 21 Jun 2020 20:59:03: 3000000 INFO @ Sun, 21 Jun 2020 20:59:08: 4000000 INFO @ Sun, 21 Jun 2020 20:59:14: 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 @ Sun, 21 Jun 2020 20:59:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX474523/SRX474523.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX474523/SRX474523.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX474523/SRX474523.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX474523/SRX474523.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 20:59:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:59:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:59:19: 6000000 INFO @ Sun, 21 Jun 2020 20:59:22: 1000000 INFO @ Sun, 21 Jun 2020 20:59:26: 7000000 INFO @ Sun, 21 Jun 2020 20:59:29: 2000000 INFO @ Sun, 21 Jun 2020 20:59:32: 8000000 INFO @ Sun, 21 Jun 2020 20:59:35: 3000000 INFO @ Sun, 21 Jun 2020 20:59:37: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:59:37: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:59:37: #1 total tags in treatment: 8769092 INFO @ Sun, 21 Jun 2020 20:59:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:59:37: #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 20:59:38: #1 tags after filtering in treatment: 8769090 INFO @ Sun, 21 Jun 2020 20:59:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:59:38: #1 finished! INFO @ Sun, 21 Jun 2020 20:59:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:59:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:59:38: #2 number of paired peaks: 669 WARNING @ Sun, 21 Jun 2020 20:59:38: Fewer paired peaks (669) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 669 pairs to build model! INFO @ Sun, 21 Jun 2020 20:59:38: start model_add_line... INFO @ Sun, 21 Jun 2020 20:59:38: start X-correlation... INFO @ Sun, 21 Jun 2020 20:59:38: end of X-cor INFO @ Sun, 21 Jun 2020 20:59:38: #2 finished! INFO @ Sun, 21 Jun 2020 20:59:38: #2 predicted fragment length is 43 bps INFO @ Sun, 21 Jun 2020 20:59:38: #2 alternative fragment length(s) may be 4,43 bps INFO @ Sun, 21 Jun 2020 20:59:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX474523/SRX474523.05_model.r WARNING @ Sun, 21 Jun 2020 20:59:38: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:59:38: #2 You may need to consider one of the other alternative d(s): 4,43 WARNING @ Sun, 21 Jun 2020 20:59:38: #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 20:59:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:59:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:59:41: 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 @ Sun, 21 Jun 2020 20:59:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX474523/SRX474523.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX474523/SRX474523.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX474523/SRX474523.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX474523/SRX474523.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 20:59:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:59:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:59:47: 5000000 INFO @ Sun, 21 Jun 2020 20:59:53: 1000000 INFO @ Sun, 21 Jun 2020 20:59:53: 6000000 INFO @ Sun, 21 Jun 2020 20:59:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:59:59: 2000000 INFO @ Sun, 21 Jun 2020 20:59:59: 7000000 INFO @ Sun, 21 Jun 2020 21:00:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX474523/SRX474523.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:00:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX474523/SRX474523.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:00:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX474523/SRX474523.05_summits.bed INFO @ Sun, 21 Jun 2020 21:00:05: Done! INFO @ Sun, 21 Jun 2020 21:00:05: 3000000 pass1 - making usageList (550 chroms): 1 millis pass2 - checking and writing primary data (2419 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:00:06: 8000000 INFO @ Sun, 21 Jun 2020 21:00:11: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:00:11: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:00:11: #1 total tags in treatment: 8769092 INFO @ Sun, 21 Jun 2020 21:00:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:00:11: #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 21:00:11: #1 tags after filtering in treatment: 8769090 INFO @ Sun, 21 Jun 2020 21:00:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:00:11: #1 finished! INFO @ Sun, 21 Jun 2020 21:00:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:00:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:00:11: 4000000 INFO @ Sun, 21 Jun 2020 21:00:12: #2 number of paired peaks: 669 WARNING @ Sun, 21 Jun 2020 21:00:12: Fewer paired peaks (669) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 669 pairs to build model! INFO @ Sun, 21 Jun 2020 21:00:12: start model_add_line... INFO @ Sun, 21 Jun 2020 21:00:12: start X-correlation... INFO @ Sun, 21 Jun 2020 21:00:12: end of X-cor INFO @ Sun, 21 Jun 2020 21:00:12: #2 finished! INFO @ Sun, 21 Jun 2020 21:00:12: #2 predicted fragment length is 43 bps INFO @ Sun, 21 Jun 2020 21:00:12: #2 alternative fragment length(s) may be 4,43 bps INFO @ Sun, 21 Jun 2020 21:00:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX474523/SRX474523.10_model.r WARNING @ Sun, 21 Jun 2020 21:00:12: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:00:12: #2 You may need to consider one of the other alternative d(s): 4,43 WARNING @ Sun, 21 Jun 2020 21:00:12: #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 21:00:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:00:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:00:17: 5000000 INFO @ Sun, 21 Jun 2020 21:00:23: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:00:29: 7000000 INFO @ Sun, 21 Jun 2020 21:00:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:00:34: 8000000 INFO @ Sun, 21 Jun 2020 21:00:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX474523/SRX474523.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:00:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX474523/SRX474523.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:00:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX474523/SRX474523.10_summits.bed INFO @ Sun, 21 Jun 2020 21:00:38: Done! pass1 - making usageList (454 chroms): 1 millis pass2 - checking and writing primary data (1602 records, 4 fields): 33 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:00:39: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:00:39: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:00:39: #1 total tags in treatment: 8769092 INFO @ Sun, 21 Jun 2020 21:00:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:00:39: #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 21:00:39: #1 tags after filtering in treatment: 8769090 INFO @ Sun, 21 Jun 2020 21:00:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:00:39: #1 finished! INFO @ Sun, 21 Jun 2020 21:00:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:00:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:00:40: #2 number of paired peaks: 669 WARNING @ Sun, 21 Jun 2020 21:00:40: Fewer paired peaks (669) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 669 pairs to build model! INFO @ Sun, 21 Jun 2020 21:00:40: start model_add_line... INFO @ Sun, 21 Jun 2020 21:00:40: start X-correlation... INFO @ Sun, 21 Jun 2020 21:00:40: end of X-cor INFO @ Sun, 21 Jun 2020 21:00:40: #2 finished! INFO @ Sun, 21 Jun 2020 21:00:40: #2 predicted fragment length is 43 bps INFO @ Sun, 21 Jun 2020 21:00:40: #2 alternative fragment length(s) may be 4,43 bps INFO @ Sun, 21 Jun 2020 21:00:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX474523/SRX474523.20_model.r WARNING @ Sun, 21 Jun 2020 21:00:40: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:00:40: #2 You may need to consider one of the other alternative d(s): 4,43 WARNING @ Sun, 21 Jun 2020 21:00:40: #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 21:00:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:00:40: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:00:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:01:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX474523/SRX474523.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:01:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX474523/SRX474523.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:01:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX474523/SRX474523.20_summits.bed INFO @ Sun, 21 Jun 2020 21:01:05: Done! pass1 - making usageList (231 chroms): 1 millis pass2 - checking and writing primary data (483 records, 4 fields): 7 millis CompletedMACS2peakCalling