Job ID = 6459796 SRX = SRX858997 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:31:43 prefetch.2.10.7: 1) Downloading 'SRR1779553'... 2020-06-21T13:31:43 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:32:36 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:32:36 prefetch.2.10.7: 'SRR1779553' is valid 2020-06-21T13:32:36 prefetch.2.10.7: 1) 'SRR1779553' was downloaded successfully 2020-06-21T13:33:28 prefetch.2.10.7: 'SRR1779553' has 10 unresolved dependencies 2020-06-21T13:33:28 prefetch.2.10.7: 2) Downloading 'ncbi-acc:AE013599.4?vdb-ctx=refseq'... 2020-06-21T13:33:28 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:33:44 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:33:44 prefetch.2.10.7: 2) 'ncbi-acc:AE013599.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T13:33:44 prefetch.2.10.7: 3) Downloading 'ncbi-acc:AE014134.5?vdb-ctx=refseq'... 2020-06-21T13:33:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:34:05 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:34:05 prefetch.2.10.7: 3) 'ncbi-acc:AE014134.5?vdb-ctx=refseq' was downloaded successfully 2020-06-21T13:34:05 prefetch.2.10.7: 4) Downloading 'ncbi-acc:AE014135.3?vdb-ctx=refseq'... 2020-06-21T13:34:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:34:17 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:34:17 prefetch.2.10.7: 4) 'ncbi-acc:AE014135.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T13:34:17 prefetch.2.10.7: 5) Downloading 'ncbi-acc:AE014296.4?vdb-ctx=refseq'... 2020-06-21T13:34:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:34:36 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:34:36 prefetch.2.10.7: 5) 'ncbi-acc:AE014296.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T13:34:36 prefetch.2.10.7: 6) Downloading 'ncbi-acc:AE014297.2?vdb-ctx=refseq'... 2020-06-21T13:34:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:34:54 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:34:54 prefetch.2.10.7: 6) 'ncbi-acc:AE014297.2?vdb-ctx=refseq' was downloaded successfully 2020-06-21T13:34:54 prefetch.2.10.7: 7) Downloading 'ncbi-acc:AE014298.4?vdb-ctx=refseq'... 2020-06-21T13:34:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:35:11 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:35:11 prefetch.2.10.7: 7) 'ncbi-acc:AE014298.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T13:35:11 prefetch.2.10.7: 8) Downloading 'ncbi-acc:CM000457.1?vdb-ctx=refseq'... 2020-06-21T13:35:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:35:25 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:35:25 prefetch.2.10.7: 8) 'ncbi-acc:CM000457.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T13:35:25 prefetch.2.10.7: 9) Downloading 'ncbi-acc:CM000458.1?vdb-ctx=refseq'... 2020-06-21T13:35:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:35:39 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:35:39 prefetch.2.10.7: 9) 'ncbi-acc:CM000458.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T13:35:39 prefetch.2.10.7: 10) Downloading 'ncbi-acc:CM000459.1?vdb-ctx=refseq'... 2020-06-21T13:35:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:35:52 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:35:52 prefetch.2.10.7: 10) 'ncbi-acc:CM000459.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T13:35:52 prefetch.2.10.7: 11) Downloading 'ncbi-acc:FA000001.1?vdb-ctx=refseq'... 2020-06-21T13:35:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:36:09 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:36:09 prefetch.2.10.7: 11) 'ncbi-acc:FA000001.1?vdb-ctx=refseq' was downloaded successfully Read 10931433 spots for SRR1779553/SRR1779553.sra Written 10931433 spots for SRR1779553/SRR1779553.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: 00:01:48 10931433 reads; of these: 10931433 (100.00%) were unpaired; of these: 63370 (0.58%) aligned 0 times 10488668 (95.95%) aligned exactly 1 time 379395 (3.47%) aligned >1 times 99.42% overall alignment rate Time searching: 00:01:48 Overall time: 00:01:48 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 8 files... [bam_rmdupse_core] 5378 / 10868063 = 0.0005 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 22:41:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX858997/SRX858997.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX858997/SRX858997.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX858997/SRX858997.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX858997/SRX858997.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 22:41:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:41:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:41:37: 1000000 INFO @ Sun, 21 Jun 2020 22:41:42: 2000000 INFO @ Sun, 21 Jun 2020 22:41:48: 3000000 INFO @ Sun, 21 Jun 2020 22:41:53: 4000000 INFO @ Sun, 21 Jun 2020 22:41:59: 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 22:42:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX858997/SRX858997.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX858997/SRX858997.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX858997/SRX858997.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX858997/SRX858997.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 22:42:01: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:42:01: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:42:04: 6000000 INFO @ Sun, 21 Jun 2020 22:42:07: 1000000 INFO @ Sun, 21 Jun 2020 22:42:10: 7000000 INFO @ Sun, 21 Jun 2020 22:42:12: 2000000 INFO @ Sun, 21 Jun 2020 22:42:16: 8000000 INFO @ Sun, 21 Jun 2020 22:42:18: 3000000 INFO @ Sun, 21 Jun 2020 22:42:21: 9000000 INFO @ Sun, 21 Jun 2020 22:42:23: 4000000 INFO @ Sun, 21 Jun 2020 22:42:27: 10000000 INFO @ Sun, 21 Jun 2020 22:42:29: 5000000 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 22:42:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX858997/SRX858997.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX858997/SRX858997.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX858997/SRX858997.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX858997/SRX858997.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 22:42:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:42:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:42:32: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:42:32: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:42:32: #1 total tags in treatment: 10862685 INFO @ Sun, 21 Jun 2020 22:42:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:42:32: #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 22:42:33: #1 tags after filtering in treatment: 10862383 INFO @ Sun, 21 Jun 2020 22:42:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:42:33: #1 finished! INFO @ Sun, 21 Jun 2020 22:42:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:42:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:42:34: #2 number of paired peaks: 3802 INFO @ Sun, 21 Jun 2020 22:42:34: start model_add_line... INFO @ Sun, 21 Jun 2020 22:42:34: start X-correlation... INFO @ Sun, 21 Jun 2020 22:42:34: end of X-cor INFO @ Sun, 21 Jun 2020 22:42:34: #2 finished! INFO @ Sun, 21 Jun 2020 22:42:34: #2 predicted fragment length is 81 bps INFO @ Sun, 21 Jun 2020 22:42:34: #2 alternative fragment length(s) may be 81 bps INFO @ Sun, 21 Jun 2020 22:42:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX858997/SRX858997.05_model.r WARNING @ Sun, 21 Jun 2020 22:42:34: #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 22:42:34: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Sun, 21 Jun 2020 22:42:34: #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 22:42:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:42:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:42:35: 6000000 INFO @ Sun, 21 Jun 2020 22:42:36: 1000000 INFO @ Sun, 21 Jun 2020 22:42:41: 7000000 INFO @ Sun, 21 Jun 2020 22:42:41: 2000000 INFO @ Sun, 21 Jun 2020 22:42:46: 8000000 INFO @ Sun, 21 Jun 2020 22:42:46: 3000000 INFO @ Sun, 21 Jun 2020 22:42:52: 4000000 INFO @ Sun, 21 Jun 2020 22:42:52: 9000000 INFO @ Sun, 21 Jun 2020 22:42:57: 5000000 INFO @ Sun, 21 Jun 2020 22:42:58: 10000000 INFO @ Sun, 21 Jun 2020 22:43:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:43:02: 6000000 INFO @ Sun, 21 Jun 2020 22:43:03: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:43:03: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:43:03: #1 total tags in treatment: 10862685 INFO @ Sun, 21 Jun 2020 22:43:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:43:03: #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 22:43:04: #1 tags after filtering in treatment: 10862383 INFO @ Sun, 21 Jun 2020 22:43:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:43:04: #1 finished! INFO @ Sun, 21 Jun 2020 22:43:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:43:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:43:05: #2 number of paired peaks: 3802 INFO @ Sun, 21 Jun 2020 22:43:05: start model_add_line... INFO @ Sun, 21 Jun 2020 22:43:05: start X-correlation... INFO @ Sun, 21 Jun 2020 22:43:05: end of X-cor INFO @ Sun, 21 Jun 2020 22:43:05: #2 finished! INFO @ Sun, 21 Jun 2020 22:43:05: #2 predicted fragment length is 81 bps INFO @ Sun, 21 Jun 2020 22:43:05: #2 alternative fragment length(s) may be 81 bps INFO @ Sun, 21 Jun 2020 22:43:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX858997/SRX858997.10_model.r WARNING @ Sun, 21 Jun 2020 22:43:05: #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 22:43:05: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Sun, 21 Jun 2020 22:43:05: #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 22:43:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:43:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:43:07: 7000000 INFO @ Sun, 21 Jun 2020 22:43:12: 8000000 INFO @ Sun, 21 Jun 2020 22:43:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX858997/SRX858997.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:43:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX858997/SRX858997.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:43:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX858997/SRX858997.05_summits.bed INFO @ Sun, 21 Jun 2020 22:43:13: Done! pass1 - making usageList (55 chroms): 2 millis pass2 - checking and writing primary data (12757 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:43:17: 9000000 INFO @ Sun, 21 Jun 2020 22:43:22: 10000000 INFO @ Sun, 21 Jun 2020 22:43:26: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:43:26: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:43:26: #1 total tags in treatment: 10862685 INFO @ Sun, 21 Jun 2020 22:43:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:43:26: #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 22:43:27: #1 tags after filtering in treatment: 10862383 INFO @ Sun, 21 Jun 2020 22:43:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:43:27: #1 finished! INFO @ Sun, 21 Jun 2020 22:43:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:43:27: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:43:28: #2 number of paired peaks: 3802 INFO @ Sun, 21 Jun 2020 22:43:28: start model_add_line... INFO @ Sun, 21 Jun 2020 22:43:28: start X-correlation... INFO @ Sun, 21 Jun 2020 22:43:28: end of X-cor INFO @ Sun, 21 Jun 2020 22:43:28: #2 finished! INFO @ Sun, 21 Jun 2020 22:43:28: #2 predicted fragment length is 81 bps INFO @ Sun, 21 Jun 2020 22:43:28: #2 alternative fragment length(s) may be 81 bps INFO @ Sun, 21 Jun 2020 22:43:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX858997/SRX858997.20_model.r WARNING @ Sun, 21 Jun 2020 22:43:28: #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 22:43:28: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Sun, 21 Jun 2020 22:43:28: #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 22:43:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:43:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:43:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:43:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX858997/SRX858997.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:43:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX858997/SRX858997.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:43:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX858997/SRX858997.10_summits.bed INFO @ Sun, 21 Jun 2020 22:43:41: Done! pass1 - making usageList (37 chroms): 2 millis pass2 - checking and writing primary data (8655 records, 4 fields): 9 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:43:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:44:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX858997/SRX858997.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:44:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX858997/SRX858997.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:44:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX858997/SRX858997.20_summits.bed INFO @ Sun, 21 Jun 2020 22:44:06: Done! pass1 - making usageList (24 chroms): 1 millis pass2 - checking and writing primary data (4526 records, 4 fields): 9 millis CompletedMACS2peakCalling