Job ID = 6457712 SRX = SRX474521 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:10:19 prefetch.2.10.7: 1) Downloading 'SRR1174368'... 2020-06-21T12:10:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:11:55 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:11:55 prefetch.2.10.7: 'SRR1174368' is valid 2020-06-21T12:11:55 prefetch.2.10.7: 1) 'SRR1174368' was downloaded successfully 2020-06-21T12:12:47 prefetch.2.10.7: 'SRR1174368' has 10 unresolved dependencies 2020-06-21T12:12:47 prefetch.2.10.7: 2) Downloading 'ncbi-acc:AE013599.4?vdb-ctx=refseq'... 2020-06-21T12:12:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:13:05 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:13:05 prefetch.2.10.7: 2) 'ncbi-acc:AE013599.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T12:13:05 prefetch.2.10.7: 3) Downloading 'ncbi-acc:AE014134.5?vdb-ctx=refseq'... 2020-06-21T12:13:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:13:21 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:13:21 prefetch.2.10.7: 3) 'ncbi-acc:AE014134.5?vdb-ctx=refseq' was downloaded successfully 2020-06-21T12:13:21 prefetch.2.10.7: 4) Downloading 'ncbi-acc:AE014135.3?vdb-ctx=refseq'... 2020-06-21T12:13:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:13:35 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:13:35 prefetch.2.10.7: 4) 'ncbi-acc:AE014135.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T12:13:35 prefetch.2.10.7: 5) Downloading 'ncbi-acc:AE014296.4?vdb-ctx=refseq'... 2020-06-21T12:13:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:13:53 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:13:53 prefetch.2.10.7: 5) 'ncbi-acc:AE014296.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T12:13:53 prefetch.2.10.7: 6) Downloading 'ncbi-acc:AE014297.2?vdb-ctx=refseq'... 2020-06-21T12:13:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:14:10 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:14:10 prefetch.2.10.7: 6) 'ncbi-acc:AE014297.2?vdb-ctx=refseq' was downloaded successfully 2020-06-21T12:14:10 prefetch.2.10.7: 7) Downloading 'ncbi-acc:AE014298.4?vdb-ctx=refseq'... 2020-06-21T12:14:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:14:28 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:14:28 prefetch.2.10.7: 7) 'ncbi-acc:AE014298.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T12:14:28 prefetch.2.10.7: 8) Downloading 'ncbi-acc:CM000457.1?vdb-ctx=refseq'... 2020-06-21T12:14:28 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:14:43 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:14:43 prefetch.2.10.7: 8) 'ncbi-acc:CM000457.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T12:14:43 prefetch.2.10.7: 9) Downloading 'ncbi-acc:CM000458.1?vdb-ctx=refseq'... 2020-06-21T12:14:43 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:14:55 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:14:55 prefetch.2.10.7: 9) 'ncbi-acc:CM000458.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T12:14:55 prefetch.2.10.7: 10) Downloading 'ncbi-acc:CM000459.1?vdb-ctx=refseq'... 2020-06-21T12:14:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:15:09 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:15:09 prefetch.2.10.7: 10) 'ncbi-acc:CM000459.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T12:15:09 prefetch.2.10.7: 11) Downloading 'ncbi-acc:FA000001.1?vdb-ctx=refseq'... 2020-06-21T12:15:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:15:25 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:15:25 prefetch.2.10.7: 11) 'ncbi-acc:FA000001.1?vdb-ctx=refseq' was downloaded successfully Read 19525308 spots for SRR1174368/SRR1174368.sra Written 19525308 spots for SRR1174368/SRR1174368.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:50 19525308 reads; of these: 19525308 (100.00%) were unpaired; of these: 377167 (1.93%) aligned 0 times 12607602 (64.57%) aligned exactly 1 time 6540539 (33.50%) aligned >1 times 98.07% overall alignment rate Time searching: 00:04:51 Overall time: 00:04:51 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] 1572036 / 19148141 = 0.0821 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 21:26:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX474521/SRX474521.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX474521/SRX474521.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX474521/SRX474521.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX474521/SRX474521.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 21:26:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:26:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:26:51: 1000000 INFO @ Sun, 21 Jun 2020 21:26:58: 2000000 INFO @ Sun, 21 Jun 2020 21:27:04: 3000000 INFO @ Sun, 21 Jun 2020 21:27:10: 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 21:27:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX474521/SRX474521.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX474521/SRX474521.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX474521/SRX474521.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX474521/SRX474521.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 21:27:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:27:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:27:16: 5000000 INFO @ Sun, 21 Jun 2020 21:27:21: 1000000 INFO @ Sun, 21 Jun 2020 21:27:22: 6000000 INFO @ Sun, 21 Jun 2020 21:27:27: 2000000 INFO @ Sun, 21 Jun 2020 21:27:28: 7000000 INFO @ Sun, 21 Jun 2020 21:27:33: 3000000 INFO @ Sun, 21 Jun 2020 21:27:34: 8000000 INFO @ Sun, 21 Jun 2020 21:27:39: 4000000 INFO @ Sun, 21 Jun 2020 21:27:40: 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 21:27:45: 5000000 INFO @ Sun, 21 Jun 2020 21:27:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX474521/SRX474521.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX474521/SRX474521.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX474521/SRX474521.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX474521/SRX474521.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 21:27:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:27:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:27:47: 10000000 INFO @ Sun, 21 Jun 2020 21:27:51: 1000000 INFO @ Sun, 21 Jun 2020 21:27:51: 6000000 INFO @ Sun, 21 Jun 2020 21:27:53: 11000000 INFO @ Sun, 21 Jun 2020 21:27:56: 2000000 INFO @ Sun, 21 Jun 2020 21:27:57: 7000000 INFO @ Sun, 21 Jun 2020 21:27:59: 12000000 INFO @ Sun, 21 Jun 2020 21:28:01: 3000000 INFO @ Sun, 21 Jun 2020 21:28:03: 8000000 INFO @ Sun, 21 Jun 2020 21:28:05: 13000000 INFO @ Sun, 21 Jun 2020 21:28:07: 4000000 INFO @ Sun, 21 Jun 2020 21:28:09: 9000000 INFO @ Sun, 21 Jun 2020 21:28:12: 5000000 INFO @ Sun, 21 Jun 2020 21:28:12: 14000000 INFO @ Sun, 21 Jun 2020 21:28:15: 10000000 INFO @ Sun, 21 Jun 2020 21:28:17: 6000000 INFO @ Sun, 21 Jun 2020 21:28:18: 15000000 INFO @ Sun, 21 Jun 2020 21:28:21: 11000000 INFO @ Sun, 21 Jun 2020 21:28:22: 7000000 INFO @ Sun, 21 Jun 2020 21:28:24: 16000000 INFO @ Sun, 21 Jun 2020 21:28:27: 12000000 INFO @ Sun, 21 Jun 2020 21:28:28: 8000000 INFO @ Sun, 21 Jun 2020 21:28:30: 17000000 INFO @ Sun, 21 Jun 2020 21:28:33: 9000000 INFO @ Sun, 21 Jun 2020 21:28:33: 13000000 INFO @ Sun, 21 Jun 2020 21:28:34: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:28:34: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:28:34: #1 total tags in treatment: 17576105 INFO @ Sun, 21 Jun 2020 21:28:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:28:34: #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 21:28:35: #1 tags after filtering in treatment: 17576105 INFO @ Sun, 21 Jun 2020 21:28:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:28:35: #1 finished! INFO @ Sun, 21 Jun 2020 21:28:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:28:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:28:36: #2 number of paired peaks: 882 WARNING @ Sun, 21 Jun 2020 21:28:36: Fewer paired peaks (882) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 882 pairs to build model! INFO @ Sun, 21 Jun 2020 21:28:36: start model_add_line... INFO @ Sun, 21 Jun 2020 21:28:36: start X-correlation... INFO @ Sun, 21 Jun 2020 21:28:36: end of X-cor INFO @ Sun, 21 Jun 2020 21:28:36: #2 finished! INFO @ Sun, 21 Jun 2020 21:28:36: #2 predicted fragment length is 68 bps INFO @ Sun, 21 Jun 2020 21:28:36: #2 alternative fragment length(s) may be 4,68 bps INFO @ Sun, 21 Jun 2020 21:28:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX474521/SRX474521.05_model.r WARNING @ Sun, 21 Jun 2020 21:28:36: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:28:36: #2 You may need to consider one of the other alternative d(s): 4,68 WARNING @ Sun, 21 Jun 2020 21:28:36: #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 21:28:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:28:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:28:38: 10000000 INFO @ Sun, 21 Jun 2020 21:28:40: 14000000 INFO @ Sun, 21 Jun 2020 21:28:44: 11000000 INFO @ Sun, 21 Jun 2020 21:28:46: 15000000 INFO @ Sun, 21 Jun 2020 21:28:49: 12000000 INFO @ Sun, 21 Jun 2020 21:28:52: 16000000 INFO @ Sun, 21 Jun 2020 21:28:54: 13000000 INFO @ Sun, 21 Jun 2020 21:28:58: 17000000 INFO @ Sun, 21 Jun 2020 21:29:00: 14000000 INFO @ Sun, 21 Jun 2020 21:29:01: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:29:01: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:29:01: #1 total tags in treatment: 17576105 INFO @ Sun, 21 Jun 2020 21:29:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:29:01: #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 21:29:02: #1 tags after filtering in treatment: 17576105 INFO @ Sun, 21 Jun 2020 21:29:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:29:02: #1 finished! INFO @ Sun, 21 Jun 2020 21:29:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:29:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:29:03: #2 number of paired peaks: 882 WARNING @ Sun, 21 Jun 2020 21:29:03: Fewer paired peaks (882) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 882 pairs to build model! INFO @ Sun, 21 Jun 2020 21:29:03: start model_add_line... INFO @ Sun, 21 Jun 2020 21:29:03: start X-correlation... INFO @ Sun, 21 Jun 2020 21:29:03: end of X-cor INFO @ Sun, 21 Jun 2020 21:29:03: #2 finished! INFO @ Sun, 21 Jun 2020 21:29:03: #2 predicted fragment length is 68 bps INFO @ Sun, 21 Jun 2020 21:29:03: #2 alternative fragment length(s) may be 4,68 bps INFO @ Sun, 21 Jun 2020 21:29:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX474521/SRX474521.10_model.r WARNING @ Sun, 21 Jun 2020 21:29:03: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:29:03: #2 You may need to consider one of the other alternative d(s): 4,68 WARNING @ Sun, 21 Jun 2020 21:29:03: #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 21:29:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:29:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:29:05: 15000000 INFO @ Sun, 21 Jun 2020 21:29:10: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:29:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:29:16: 17000000 INFO @ Sun, 21 Jun 2020 21:29:19: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:29:19: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:29:19: #1 total tags in treatment: 17576105 INFO @ Sun, 21 Jun 2020 21:29:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:29:19: #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 21:29:20: #1 tags after filtering in treatment: 17576105 INFO @ Sun, 21 Jun 2020 21:29:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:29:20: #1 finished! INFO @ Sun, 21 Jun 2020 21:29:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:29:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:29:21: #2 number of paired peaks: 882 WARNING @ Sun, 21 Jun 2020 21:29:21: Fewer paired peaks (882) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 882 pairs to build model! INFO @ Sun, 21 Jun 2020 21:29:21: start model_add_line... INFO @ Sun, 21 Jun 2020 21:29:21: start X-correlation... INFO @ Sun, 21 Jun 2020 21:29:21: end of X-cor INFO @ Sun, 21 Jun 2020 21:29:21: #2 finished! INFO @ Sun, 21 Jun 2020 21:29:21: #2 predicted fragment length is 68 bps INFO @ Sun, 21 Jun 2020 21:29:21: #2 alternative fragment length(s) may be 4,68 bps INFO @ Sun, 21 Jun 2020 21:29:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX474521/SRX474521.20_model.r WARNING @ Sun, 21 Jun 2020 21:29:21: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:29:21: #2 You may need to consider one of the other alternative d(s): 4,68 WARNING @ Sun, 21 Jun 2020 21:29:21: #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 21:29:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:29:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:29:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX474521/SRX474521.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:29:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX474521/SRX474521.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:29:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX474521/SRX474521.05_summits.bed INFO @ Sun, 21 Jun 2020 21:29:32: Done! pass1 - making usageList (778 chroms): 2 millis pass2 - checking and writing primary data (5286 records, 4 fields): 39 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:29:40: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:29:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:29:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX474521/SRX474521.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:29:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX474521/SRX474521.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:29:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX474521/SRX474521.10_summits.bed INFO @ Sun, 21 Jun 2020 21:29:59: Done! pass1 - making usageList (652 chroms): 1 millis pass2 - checking and writing primary data (3129 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:30:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX474521/SRX474521.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:30:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX474521/SRX474521.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:30:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX474521/SRX474521.20_summits.bed INFO @ Sun, 21 Jun 2020 21:30:15: Done! pass1 - making usageList (510 chroms): 1 millis pass2 - checking and writing primary data (1678 records, 4 fields): 18 millis CompletedMACS2peakCalling