Job ID = 6454428 SRX = SRX2055956 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:13:40 prefetch.2.10.7: 1) Downloading 'SRR4069188'... 2020-06-21T09:13:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:17:48 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:17:49 prefetch.2.10.7: 'SRR4069188' is valid 2020-06-21T09:17:49 prefetch.2.10.7: 1) 'SRR4069188' was downloaded successfully Read 21646028 spots for SRR4069188/SRR4069188.sra Written 21646028 spots for SRR4069188/SRR4069188.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: 00:06:43 21646028 reads; of these: 21646028 (100.00%) were unpaired; of these: 956288 (4.42%) aligned 0 times 13456725 (62.17%) aligned exactly 1 time 7233015 (33.41%) aligned >1 times 95.58% overall alignment rate Time searching: 00:06:43 Overall time: 00:06:43 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] 3570361 / 20689740 = 0.1726 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 18:29:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2055956/SRX2055956.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2055956/SRX2055956.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2055956/SRX2055956.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2055956/SRX2055956.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 18:29:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:29:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:29:50: 1000000 INFO @ Sun, 21 Jun 2020 18:29:57: 2000000 INFO @ Sun, 21 Jun 2020 18:30:03: 3000000 INFO @ Sun, 21 Jun 2020 18:30:09: 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 18:30:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2055956/SRX2055956.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2055956/SRX2055956.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2055956/SRX2055956.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2055956/SRX2055956.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 18:30:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:30:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:30:15: 5000000 INFO @ Sun, 21 Jun 2020 18:30:20: 1000000 INFO @ Sun, 21 Jun 2020 18:30:21: 6000000 INFO @ Sun, 21 Jun 2020 18:30:26: 2000000 INFO @ Sun, 21 Jun 2020 18:30:28: 7000000 INFO @ Sun, 21 Jun 2020 18:30:32: 3000000 INFO @ Sun, 21 Jun 2020 18:30:34: 8000000 INFO @ Sun, 21 Jun 2020 18:30:38: 4000000 INFO @ Sun, 21 Jun 2020 18:30:41: 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 18:30:44: 5000000 INFO @ Sun, 21 Jun 2020 18:30:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2055956/SRX2055956.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2055956/SRX2055956.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2055956/SRX2055956.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2055956/SRX2055956.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 18:30:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:30:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:30:47: 10000000 INFO @ Sun, 21 Jun 2020 18:30:50: 6000000 INFO @ Sun, 21 Jun 2020 18:30:51: 1000000 INFO @ Sun, 21 Jun 2020 18:30:53: 11000000 INFO @ Sun, 21 Jun 2020 18:30:56: 7000000 INFO @ Sun, 21 Jun 2020 18:30:57: 2000000 INFO @ Sun, 21 Jun 2020 18:31:00: 12000000 INFO @ Sun, 21 Jun 2020 18:31:01: 8000000 INFO @ Sun, 21 Jun 2020 18:31:04: 3000000 INFO @ Sun, 21 Jun 2020 18:31:07: 13000000 INFO @ Sun, 21 Jun 2020 18:31:07: 9000000 INFO @ Sun, 21 Jun 2020 18:31:10: 4000000 INFO @ Sun, 21 Jun 2020 18:31:13: 10000000 INFO @ Sun, 21 Jun 2020 18:31:14: 14000000 INFO @ Sun, 21 Jun 2020 18:31:17: 5000000 INFO @ Sun, 21 Jun 2020 18:31:19: 11000000 INFO @ Sun, 21 Jun 2020 18:31:21: 15000000 INFO @ Sun, 21 Jun 2020 18:31:23: 6000000 INFO @ Sun, 21 Jun 2020 18:31:25: 12000000 INFO @ Sun, 21 Jun 2020 18:31:27: 16000000 INFO @ Sun, 21 Jun 2020 18:31:30: 7000000 INFO @ Sun, 21 Jun 2020 18:31:31: 13000000 INFO @ Sun, 21 Jun 2020 18:31:34: 17000000 INFO @ Sun, 21 Jun 2020 18:31:35: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:31:35: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:31:35: #1 total tags in treatment: 17119379 INFO @ Sun, 21 Jun 2020 18:31:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:31:35: #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 18:31:35: #1 tags after filtering in treatment: 17119311 INFO @ Sun, 21 Jun 2020 18:31:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:31:35: #1 finished! INFO @ Sun, 21 Jun 2020 18:31:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:31:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:31:36: 8000000 INFO @ Sun, 21 Jun 2020 18:31:36: 14000000 INFO @ Sun, 21 Jun 2020 18:31:37: #2 number of paired peaks: 1875 INFO @ Sun, 21 Jun 2020 18:31:37: start model_add_line... INFO @ Sun, 21 Jun 2020 18:31:37: start X-correlation... INFO @ Sun, 21 Jun 2020 18:31:37: end of X-cor INFO @ Sun, 21 Jun 2020 18:31:37: #2 finished! INFO @ Sun, 21 Jun 2020 18:31:37: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 18:31:37: #2 alternative fragment length(s) may be 2,47 bps INFO @ Sun, 21 Jun 2020 18:31:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2055956/SRX2055956.05_model.r WARNING @ Sun, 21 Jun 2020 18:31:37: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:31:37: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Sun, 21 Jun 2020 18:31:37: #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 18:31:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:31:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:31:42: 9000000 INFO @ Sun, 21 Jun 2020 18:31:43: 15000000 INFO @ Sun, 21 Jun 2020 18:31:48: 16000000 INFO @ Sun, 21 Jun 2020 18:31:49: 10000000 INFO @ Sun, 21 Jun 2020 18:31:54: 17000000 INFO @ Sun, 21 Jun 2020 18:31:55: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:31:55: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:31:55: #1 total tags in treatment: 17119379 INFO @ Sun, 21 Jun 2020 18:31:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:31:55: #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 18:31:55: 11000000 INFO @ Sun, 21 Jun 2020 18:31:56: #1 tags after filtering in treatment: 17119311 INFO @ Sun, 21 Jun 2020 18:31:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:31:56: #1 finished! INFO @ Sun, 21 Jun 2020 18:31:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:31:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:31:57: #2 number of paired peaks: 1875 INFO @ Sun, 21 Jun 2020 18:31:57: start model_add_line... INFO @ Sun, 21 Jun 2020 18:31:57: start X-correlation... INFO @ Sun, 21 Jun 2020 18:31:57: end of X-cor INFO @ Sun, 21 Jun 2020 18:31:57: #2 finished! INFO @ Sun, 21 Jun 2020 18:31:57: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 18:31:57: #2 alternative fragment length(s) may be 2,47 bps INFO @ Sun, 21 Jun 2020 18:31:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2055956/SRX2055956.10_model.r WARNING @ Sun, 21 Jun 2020 18:31:57: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:31:57: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Sun, 21 Jun 2020 18:31:57: #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 18:31:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:31:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:32:01: 12000000 INFO @ Sun, 21 Jun 2020 18:32:07: 13000000 INFO @ Sun, 21 Jun 2020 18:32:09: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:32:14: 14000000 INFO @ Sun, 21 Jun 2020 18:32:20: 15000000 INFO @ Sun, 21 Jun 2020 18:32:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2055956/SRX2055956.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:32:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2055956/SRX2055956.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:32:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2055956/SRX2055956.05_summits.bed INFO @ Sun, 21 Jun 2020 18:32:25: Done! pass1 - making usageList (671 chroms): 2 millis pass2 - checking and writing primary data (3084 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:32:26: 16000000 INFO @ Sun, 21 Jun 2020 18:32:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:32:32: 17000000 INFO @ Sun, 21 Jun 2020 18:32:33: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:32:33: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:32:33: #1 total tags in treatment: 17119379 INFO @ Sun, 21 Jun 2020 18:32:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:32:33: #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 18:32:33: #1 tags after filtering in treatment: 17119311 INFO @ Sun, 21 Jun 2020 18:32:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:32:33: #1 finished! INFO @ Sun, 21 Jun 2020 18:32:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:32:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:32:35: #2 number of paired peaks: 1875 INFO @ Sun, 21 Jun 2020 18:32:35: start model_add_line... INFO @ Sun, 21 Jun 2020 18:32:35: start X-correlation... INFO @ Sun, 21 Jun 2020 18:32:35: end of X-cor INFO @ Sun, 21 Jun 2020 18:32:35: #2 finished! INFO @ Sun, 21 Jun 2020 18:32:35: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 18:32:35: #2 alternative fragment length(s) may be 2,47 bps INFO @ Sun, 21 Jun 2020 18:32:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2055956/SRX2055956.20_model.r WARNING @ Sun, 21 Jun 2020 18:32:35: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:32:35: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Sun, 21 Jun 2020 18:32:35: #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 18:32:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:32:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:32:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2055956/SRX2055956.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:32:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2055956/SRX2055956.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:32:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2055956/SRX2055956.10_summits.bed INFO @ Sun, 21 Jun 2020 18:32:44: Done! pass1 - making usageList (548 chroms): 1 millis pass2 - checking and writing primary data (2201 records, 4 fields): 16 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:33:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:33:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2055956/SRX2055956.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:33:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2055956/SRX2055956.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:33:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2055956/SRX2055956.20_summits.bed INFO @ Sun, 21 Jun 2020 18:33:23: Done! pass1 - making usageList (438 chroms): 1 millis pass2 - checking and writing primary data (1493 records, 4 fields): 13 millis CompletedMACS2peakCalling