Job ID = 6453996 SRX = SRX1760700 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:59:49 prefetch.2.10.7: 1) Downloading 'SRR3503059'... 2020-06-21T08:59:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:01:18 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:01:19 prefetch.2.10.7: 'SRR3503059' is valid 2020-06-21T09:01:19 prefetch.2.10.7: 1) 'SRR3503059' was downloaded successfully 2020-06-21T09:01:19 prefetch.2.10.7: 'SRR3503059' has 0 unresolved dependencies Read 4248409 spots for SRR3503059/SRR3503059.sra Written 4248409 spots for SRR3503059/SRR3503059.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:43 4248409 reads; of these: 4248409 (100.00%) were unpaired; of these: 1323026 (31.14%) aligned 0 times 821956 (19.35%) aligned exactly 1 time 2103427 (49.51%) aligned >1 times 68.86% overall alignment rate Time searching: 00:05:44 Overall time: 00:05:44 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] 473255 / 2925383 = 0.1618 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 18:09:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1760700/SRX1760700.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1760700/SRX1760700.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1760700/SRX1760700.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1760700/SRX1760700.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 18:09:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:09:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:09:12: 1000000 INFO @ Sun, 21 Jun 2020 18:09:23: 2000000 INFO @ Sun, 21 Jun 2020 18:09:27: #1 tag size is determined as 151 bps INFO @ Sun, 21 Jun 2020 18:09:27: #1 tag size = 151 INFO @ Sun, 21 Jun 2020 18:09:27: #1 total tags in treatment: 2452128 INFO @ Sun, 21 Jun 2020 18:09:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:09:27: #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 18:09:27: #1 tags after filtering in treatment: 2451942 INFO @ Sun, 21 Jun 2020 18:09:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:09:27: #1 finished! INFO @ Sun, 21 Jun 2020 18:09:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:09:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:09:28: #2 number of paired peaks: 5362 INFO @ Sun, 21 Jun 2020 18:09:28: start model_add_line... INFO @ Sun, 21 Jun 2020 18:09:28: start X-correlation... INFO @ Sun, 21 Jun 2020 18:09:28: end of X-cor INFO @ Sun, 21 Jun 2020 18:09:28: #2 finished! INFO @ Sun, 21 Jun 2020 18:09:28: #2 predicted fragment length is 146 bps INFO @ Sun, 21 Jun 2020 18:09:28: #2 alternative fragment length(s) may be 146 bps INFO @ Sun, 21 Jun 2020 18:09:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1760700/SRX1760700.05_model.r WARNING @ Sun, 21 Jun 2020 18:09:28: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:09:28: #2 You may need to consider one of the other alternative d(s): 146 WARNING @ Sun, 21 Jun 2020 18:09:28: #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 18:09:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:09:28: #3 Pre-compute pvalue-qvalue table... 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 18:09:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1760700/SRX1760700.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1760700/SRX1760700.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1760700/SRX1760700.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1760700/SRX1760700.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 18:09:32: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:09:32: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:09:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:09:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1760700/SRX1760700.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:09:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1760700/SRX1760700.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:09:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1760700/SRX1760700.05_summits.bed INFO @ Sun, 21 Jun 2020 18:09:37: Done! pass1 - making usageList (797 chroms): 1 millis pass2 - checking and writing primary data (2378 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:09:43: 1000000 INFO @ Sun, 21 Jun 2020 18:09:53: 2000000 INFO @ Sun, 21 Jun 2020 18:09:57: #1 tag size is determined as 151 bps INFO @ Sun, 21 Jun 2020 18:09:57: #1 tag size = 151 INFO @ Sun, 21 Jun 2020 18:09:57: #1 total tags in treatment: 2452128 INFO @ Sun, 21 Jun 2020 18:09:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:09:57: #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 18:09:58: #1 tags after filtering in treatment: 2451942 INFO @ Sun, 21 Jun 2020 18:09:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:09:58: #1 finished! INFO @ Sun, 21 Jun 2020 18:09:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:09:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:09:58: #2 number of paired peaks: 5362 INFO @ Sun, 21 Jun 2020 18:09:58: start model_add_line... INFO @ Sun, 21 Jun 2020 18:09:58: start X-correlation... INFO @ Sun, 21 Jun 2020 18:09:58: end of X-cor INFO @ Sun, 21 Jun 2020 18:09:58: #2 finished! INFO @ Sun, 21 Jun 2020 18:09:58: #2 predicted fragment length is 146 bps INFO @ Sun, 21 Jun 2020 18:09:58: #2 alternative fragment length(s) may be 146 bps INFO @ Sun, 21 Jun 2020 18:09:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1760700/SRX1760700.10_model.r WARNING @ Sun, 21 Jun 2020 18:09:58: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:09:58: #2 You may need to consider one of the other alternative d(s): 146 WARNING @ Sun, 21 Jun 2020 18:09:58: #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 18:09:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:09:58: #3 Pre-compute pvalue-qvalue table... 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 18:10:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1760700/SRX1760700.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1760700/SRX1760700.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1760700/SRX1760700.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1760700/SRX1760700.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 18:10:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:10:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:10:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:10:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1760700/SRX1760700.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:10:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1760700/SRX1760700.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:10:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1760700/SRX1760700.10_summits.bed INFO @ Sun, 21 Jun 2020 18:10:08: Done! pass1 - making usageList (715 chroms): 1 millis pass2 - checking and writing primary data (1713 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:10:13: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:10:23: 2000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:10:28: #1 tag size is determined as 151 bps INFO @ Sun, 21 Jun 2020 18:10:28: #1 tag size = 151 INFO @ Sun, 21 Jun 2020 18:10:28: #1 total tags in treatment: 2452128 INFO @ Sun, 21 Jun 2020 18:10:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:10:28: #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 18:10:28: #1 tags after filtering in treatment: 2451942 INFO @ Sun, 21 Jun 2020 18:10:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:10:28: #1 finished! INFO @ Sun, 21 Jun 2020 18:10:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:10:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:10:29: #2 number of paired peaks: 5362 INFO @ Sun, 21 Jun 2020 18:10:29: start model_add_line... INFO @ Sun, 21 Jun 2020 18:10:29: start X-correlation... INFO @ Sun, 21 Jun 2020 18:10:29: end of X-cor INFO @ Sun, 21 Jun 2020 18:10:29: #2 finished! INFO @ Sun, 21 Jun 2020 18:10:29: #2 predicted fragment length is 146 bps INFO @ Sun, 21 Jun 2020 18:10:29: #2 alternative fragment length(s) may be 146 bps INFO @ Sun, 21 Jun 2020 18:10:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1760700/SRX1760700.20_model.r WARNING @ Sun, 21 Jun 2020 18:10:29: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:10:29: #2 You may need to consider one of the other alternative d(s): 146 WARNING @ Sun, 21 Jun 2020 18:10:29: #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 18:10:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:10:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:10:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:10:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1760700/SRX1760700.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:10:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1760700/SRX1760700.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:10:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1760700/SRX1760700.20_summits.bed INFO @ Sun, 21 Jun 2020 18:10:38: Done! pass1 - making usageList (623 chroms): 1 millis pass2 - checking and writing primary data (1170 records, 4 fields): 17 millis CompletedMACS2peakCalling