Job ID = 6457025 SRX = SRX4315047 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:18:09 prefetch.2.10.7: 1) Downloading 'SRR7444508'... 2020-06-21T11:18:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:19:20 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:19:21 prefetch.2.10.7: 'SRR7444508' is valid 2020-06-21T11:19:21 prefetch.2.10.7: 1) 'SRR7444508' was downloaded successfully 2020-06-21T11:20:02 prefetch.2.10.7: 'SRR7444508' has 7 unresolved dependencies 2020-06-21T11:20:02 prefetch.2.10.7: 2) Downloading 'ncbi-acc:AE013599.5?vdb-ctx=refseq'... 2020-06-21T11:20:02 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:20:21 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:20:21 prefetch.2.10.7: 2) 'ncbi-acc:AE013599.5?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:20:21 prefetch.2.10.7: 3) Downloading 'ncbi-acc:AE014134.6?vdb-ctx=refseq'... 2020-06-21T11:20:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:20:38 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:20:38 prefetch.2.10.7: 3) 'ncbi-acc:AE014134.6?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:20:38 prefetch.2.10.7: 4) Downloading 'ncbi-acc:AE014135.4?vdb-ctx=refseq'... 2020-06-21T11:20:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:20:51 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:20:51 prefetch.2.10.7: 4) 'ncbi-acc:AE014135.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:20:51 prefetch.2.10.7: 5) Downloading 'ncbi-acc:AE014296.5?vdb-ctx=refseq'... 2020-06-21T11:20:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:21:13 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:21:13 prefetch.2.10.7: 5) 'ncbi-acc:AE014296.5?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:21:13 prefetch.2.10.7: 6) Downloading 'ncbi-acc:AE014297.3?vdb-ctx=refseq'... 2020-06-21T11:21:13 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:21:35 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:21:35 prefetch.2.10.7: 6) 'ncbi-acc:AE014297.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:21:35 prefetch.2.10.7: 7) Downloading 'ncbi-acc:AE014298.5?vdb-ctx=refseq'... 2020-06-21T11:21:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:21:53 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:21:53 prefetch.2.10.7: 7) 'ncbi-acc:AE014298.5?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:21:53 prefetch.2.10.7: 8) Downloading 'ncbi-acc:CP007106.1?vdb-ctx=refseq'... 2020-06-21T11:21:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:22:08 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:22:08 prefetch.2.10.7: 8) 'ncbi-acc:CP007106.1?vdb-ctx=refseq' was downloaded successfully Read 20443155 spots for SRR7444508/SRR7444508.sra Written 20443155 spots for SRR7444508/SRR7444508.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: 00:05:00 20443155 reads; of these: 20443155 (100.00%) were unpaired; of these: 12333 (0.06%) aligned 0 times 17928135 (87.70%) aligned exactly 1 time 2502687 (12.24%) aligned >1 times 99.94% overall alignment rate Time searching: 00:05:01 Overall time: 00:05:01 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_sort_core] merging from 12 files... [bam_rmdupse_core] 9216634 / 20430822 = 0.4511 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 20:33:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4315047/SRX4315047.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4315047/SRX4315047.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4315047/SRX4315047.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4315047/SRX4315047.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 20:33:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:33:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:33:15: 1000000 INFO @ Sun, 21 Jun 2020 20:33:21: 2000000 INFO @ Sun, 21 Jun 2020 20:33:27: 3000000 INFO @ Sun, 21 Jun 2020 20:33:33: 4000000 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 20:33:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4315047/SRX4315047.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4315047/SRX4315047.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4315047/SRX4315047.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4315047/SRX4315047.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 20:33:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:33:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:33:39: 5000000 INFO @ Sun, 21 Jun 2020 20:33:46: 1000000 INFO @ Sun, 21 Jun 2020 20:33:46: 6000000 INFO @ Sun, 21 Jun 2020 20:33:52: 2000000 INFO @ Sun, 21 Jun 2020 20:33:53: 7000000 INFO @ Sun, 21 Jun 2020 20:33:59: 3000000 INFO @ Sun, 21 Jun 2020 20:34:00: 8000000 INFO @ Sun, 21 Jun 2020 20:34:06: 4000000 INFO @ Sun, 21 Jun 2020 20:34:07: 9000000 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 20:34:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4315047/SRX4315047.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4315047/SRX4315047.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4315047/SRX4315047.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4315047/SRX4315047.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 20:34:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:34:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:34:13: 5000000 INFO @ Sun, 21 Jun 2020 20:34:13: 10000000 INFO @ Sun, 21 Jun 2020 20:34:16: 1000000 INFO @ Sun, 21 Jun 2020 20:34:20: 6000000 INFO @ Sun, 21 Jun 2020 20:34:20: 11000000 INFO @ Sun, 21 Jun 2020 20:34:22: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 20:34:22: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 20:34:22: #1 total tags in treatment: 11214188 INFO @ Sun, 21 Jun 2020 20:34:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:34:22: #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 20:34:22: #1 tags after filtering in treatment: 11214018 INFO @ Sun, 21 Jun 2020 20:34:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:34:22: #1 finished! INFO @ Sun, 21 Jun 2020 20:34:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:34:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:34:23: 2000000 INFO @ Sun, 21 Jun 2020 20:34:23: #2 number of paired peaks: 639 WARNING @ Sun, 21 Jun 2020 20:34:23: Fewer paired peaks (639) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 639 pairs to build model! INFO @ Sun, 21 Jun 2020 20:34:23: start model_add_line... INFO @ Sun, 21 Jun 2020 20:34:23: start X-correlation... INFO @ Sun, 21 Jun 2020 20:34:23: end of X-cor INFO @ Sun, 21 Jun 2020 20:34:23: #2 finished! INFO @ Sun, 21 Jun 2020 20:34:23: #2 predicted fragment length is 100 bps INFO @ Sun, 21 Jun 2020 20:34:23: #2 alternative fragment length(s) may be 100 bps INFO @ Sun, 21 Jun 2020 20:34:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4315047/SRX4315047.05_model.r WARNING @ Sun, 21 Jun 2020 20:34:23: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:34:23: #2 You may need to consider one of the other alternative d(s): 100 WARNING @ Sun, 21 Jun 2020 20:34:23: #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 20:34:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:34:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:34:27: 7000000 INFO @ Sun, 21 Jun 2020 20:34:29: 3000000 INFO @ Sun, 21 Jun 2020 20:34:33: 8000000 INFO @ Sun, 21 Jun 2020 20:34:36: 4000000 INFO @ Sun, 21 Jun 2020 20:34:40: 9000000 INFO @ Sun, 21 Jun 2020 20:34:43: 5000000 INFO @ Sun, 21 Jun 2020 20:34:47: 10000000 INFO @ Sun, 21 Jun 2020 20:34:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:34:50: 6000000 INFO @ Sun, 21 Jun 2020 20:34:54: 11000000 INFO @ Sun, 21 Jun 2020 20:34:55: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 20:34:55: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 20:34:55: #1 total tags in treatment: 11214188 INFO @ Sun, 21 Jun 2020 20:34:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:34:55: #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 20:34:56: #1 tags after filtering in treatment: 11214018 INFO @ Sun, 21 Jun 2020 20:34:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:34:56: #1 finished! INFO @ Sun, 21 Jun 2020 20:34:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:34:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:34:56: #2 number of paired peaks: 639 WARNING @ Sun, 21 Jun 2020 20:34:56: Fewer paired peaks (639) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 639 pairs to build model! INFO @ Sun, 21 Jun 2020 20:34:56: start model_add_line... INFO @ Sun, 21 Jun 2020 20:34:57: 7000000 INFO @ Sun, 21 Jun 2020 20:34:57: start X-correlation... INFO @ Sun, 21 Jun 2020 20:34:57: end of X-cor INFO @ Sun, 21 Jun 2020 20:34:57: #2 finished! INFO @ Sun, 21 Jun 2020 20:34:57: #2 predicted fragment length is 100 bps INFO @ Sun, 21 Jun 2020 20:34:57: #2 alternative fragment length(s) may be 100 bps INFO @ Sun, 21 Jun 2020 20:34:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4315047/SRX4315047.10_model.r WARNING @ Sun, 21 Jun 2020 20:34:57: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:34:57: #2 You may need to consider one of the other alternative d(s): 100 WARNING @ Sun, 21 Jun 2020 20:34:57: #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 20:34:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:34:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:35:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4315047/SRX4315047.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:35:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4315047/SRX4315047.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:35:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4315047/SRX4315047.05_summits.bed INFO @ Sun, 21 Jun 2020 20:35:00: Done! pass1 - making usageList (206 chroms): 1 millis pass2 - checking and writing primary data (4202 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:35:03: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:35:10: 9000000 INFO @ Sun, 21 Jun 2020 20:35:15: 10000000 INFO @ Sun, 21 Jun 2020 20:35:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:35:21: 11000000 INFO @ Sun, 21 Jun 2020 20:35:23: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 20:35:23: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 20:35:23: #1 total tags in treatment: 11214188 INFO @ Sun, 21 Jun 2020 20:35:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:35:23: #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 20:35:23: #1 tags after filtering in treatment: 11214018 INFO @ Sun, 21 Jun 2020 20:35:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:35:23: #1 finished! INFO @ Sun, 21 Jun 2020 20:35:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:35:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:35:24: #2 number of paired peaks: 639 WARNING @ Sun, 21 Jun 2020 20:35:24: Fewer paired peaks (639) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 639 pairs to build model! INFO @ Sun, 21 Jun 2020 20:35:24: start model_add_line... INFO @ Sun, 21 Jun 2020 20:35:24: start X-correlation... INFO @ Sun, 21 Jun 2020 20:35:24: end of X-cor INFO @ Sun, 21 Jun 2020 20:35:24: #2 finished! INFO @ Sun, 21 Jun 2020 20:35:24: #2 predicted fragment length is 100 bps INFO @ Sun, 21 Jun 2020 20:35:24: #2 alternative fragment length(s) may be 100 bps INFO @ Sun, 21 Jun 2020 20:35:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4315047/SRX4315047.20_model.r WARNING @ Sun, 21 Jun 2020 20:35:24: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:35:24: #2 You may need to consider one of the other alternative d(s): 100 WARNING @ Sun, 21 Jun 2020 20:35:24: #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 20:35:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:35:24: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:35:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4315047/SRX4315047.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:35:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4315047/SRX4315047.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:35:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4315047/SRX4315047.10_summits.bed INFO @ Sun, 21 Jun 2020 20:35:33: Done! pass1 - making usageList (116 chroms): 2 millis pass2 - checking and writing primary data (2110 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:35:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:36:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4315047/SRX4315047.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:36:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4315047/SRX4315047.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:36:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4315047/SRX4315047.20_summits.bed INFO @ Sun, 21 Jun 2020 20:36:00: Done! pass1 - making usageList (88 chroms): 1 millis pass2 - checking and writing primary data (755 records, 4 fields): 5 millis CompletedMACS2peakCalling