Job ID = 6627092 SRX = SRX8347289 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-14T00:49:48 prefetch.2.10.7: 1) Downloading 'SRR11795472'... 2020-07-14T00:49:48 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:10:03 prefetch.2.10.7: HTTPS download failed 2020-07-14T01:10:03 prefetch.2.10.7: 1) failed to download SRR11795472 2020-07-14T01:10:17 prefetch.2.10.7: 1) Downloading 'SRR11795472'... 2020-07-14T01:10:17 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:10:17 prefetch.2.10.7: Continue download of 'SRR11795472' from 2263454596 2020-07-14T01:10:26 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:10:26 prefetch.2.10.7: 1) 'SRR11795472' was downloaded successfully 2020-07-14T01:10:26 prefetch.2.10.7: 'SRR11795472' has 0 unresolved dependencies Read 19536608 spots for SRR11795472/SRR11795472.sra Written 19536608 spots for SRR11795472/SRR11795472.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627477 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:46:04 19536608 reads; of these: 19536608 (100.00%) were paired; of these: 8930740 (45.71%) aligned concordantly 0 times 7969182 (40.79%) aligned concordantly exactly 1 time 2636686 (13.50%) aligned concordantly >1 times ---- 8930740 pairs aligned concordantly 0 times; of these: 968392 (10.84%) aligned discordantly 1 time ---- 7962348 pairs aligned 0 times concordantly or discordantly; of these: 15924696 mates make up the pairs; of these: 14945777 (93.85%) aligned 0 times 327031 (2.05%) aligned exactly 1 time 651888 (4.09%) aligned >1 times 61.75% overall alignment rate Time searching: 00:46:04 Overall time: 00:46:04 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 20 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 7093782 / 11522512 = 0.6156 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 @ Tue, 14 Jul 2020 11:06:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8347289/SRX8347289.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8347289/SRX8347289.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8347289/SRX8347289.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8347289/SRX8347289.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 @ Tue, 14 Jul 2020 11:06:23: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:06:23: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:06:31: 1000000 INFO @ Tue, 14 Jul 2020 11:06:38: 2000000 INFO @ Tue, 14 Jul 2020 11:06:45: 3000000 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 @ Tue, 14 Jul 2020 11:06:53: 4000000 INFO @ Tue, 14 Jul 2020 11:06:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8347289/SRX8347289.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8347289/SRX8347289.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8347289/SRX8347289.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8347289/SRX8347289.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 @ Tue, 14 Jul 2020 11:06:53: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:06:53: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:07:01: 5000000 INFO @ Tue, 14 Jul 2020 11:07:02: 1000000 INFO @ Tue, 14 Jul 2020 11:07:09: 6000000 INFO @ Tue, 14 Jul 2020 11:07:11: 2000000 INFO @ Tue, 14 Jul 2020 11:07:18: 7000000 INFO @ Tue, 14 Jul 2020 11:07:20: 3000000 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 @ Tue, 14 Jul 2020 11:07:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8347289/SRX8347289.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8347289/SRX8347289.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8347289/SRX8347289.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8347289/SRX8347289.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 @ Tue, 14 Jul 2020 11:07:23: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:07:23: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:07:26: 8000000 INFO @ Tue, 14 Jul 2020 11:07:28: 4000000 INFO @ Tue, 14 Jul 2020 11:07:32: 1000000 INFO @ Tue, 14 Jul 2020 11:07:36: 9000000 INFO @ Tue, 14 Jul 2020 11:07:36: 5000000 INFO @ Tue, 14 Jul 2020 11:07:41: 2000000 INFO @ Tue, 14 Jul 2020 11:07:44: #1 tag size is determined as 151 bps INFO @ Tue, 14 Jul 2020 11:07:44: #1 tag size = 151 INFO @ Tue, 14 Jul 2020 11:07:44: #1 total tags in treatment: 3948049 INFO @ Tue, 14 Jul 2020 11:07:44: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:07:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 11:07:44: #1 tags after filtering in treatment: 3791171 INFO @ Tue, 14 Jul 2020 11:07:44: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 14 Jul 2020 11:07:44: #1 finished! INFO @ Tue, 14 Jul 2020 11:07:44: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:07:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:07:44: #2 number of paired peaks: 1326 INFO @ Tue, 14 Jul 2020 11:07:44: start model_add_line... INFO @ Tue, 14 Jul 2020 11:07:44: start X-correlation... INFO @ Tue, 14 Jul 2020 11:07:44: end of X-cor INFO @ Tue, 14 Jul 2020 11:07:44: #2 finished! INFO @ Tue, 14 Jul 2020 11:07:44: #2 predicted fragment length is 235 bps INFO @ Tue, 14 Jul 2020 11:07:44: #2 alternative fragment length(s) may be 235 bps INFO @ Tue, 14 Jul 2020 11:07:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8347289/SRX8347289.05_model.r WARNING @ Tue, 14 Jul 2020 11:07:44: #2 Since the d (235) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:07:44: #2 You may need to consider one of the other alternative d(s): 235 WARNING @ Tue, 14 Jul 2020 11:07:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 11:07:44: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:07:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:07:45: 6000000 INFO @ Tue, 14 Jul 2020 11:07:50: 3000000 INFO @ Tue, 14 Jul 2020 11:07:52: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:07:53: 7000000 INFO @ Tue, 14 Jul 2020 11:07:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8347289/SRX8347289.05_peaks.xls INFO @ Tue, 14 Jul 2020 11:07:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8347289/SRX8347289.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:07:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8347289/SRX8347289.05_summits.bed INFO @ Tue, 14 Jul 2020 11:07:56: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3928 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:07:58: 4000000 INFO @ Tue, 14 Jul 2020 11:08:02: 8000000 INFO @ Tue, 14 Jul 2020 11:08:07: 5000000 INFO @ Tue, 14 Jul 2020 11:08:11: 9000000 INFO @ Tue, 14 Jul 2020 11:08:15: 6000000 INFO @ Tue, 14 Jul 2020 11:08:19: #1 tag size is determined as 151 bps INFO @ Tue, 14 Jul 2020 11:08:19: #1 tag size = 151 INFO @ Tue, 14 Jul 2020 11:08:19: #1 total tags in treatment: 3948049 INFO @ Tue, 14 Jul 2020 11:08:19: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:08:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 11:08:20: #1 tags after filtering in treatment: 3791171 INFO @ Tue, 14 Jul 2020 11:08:20: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 14 Jul 2020 11:08:20: #1 finished! INFO @ Tue, 14 Jul 2020 11:08:20: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:08:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:08:20: #2 number of paired peaks: 1326 INFO @ Tue, 14 Jul 2020 11:08:20: start model_add_line... INFO @ Tue, 14 Jul 2020 11:08:20: start X-correlation... INFO @ Tue, 14 Jul 2020 11:08:20: end of X-cor INFO @ Tue, 14 Jul 2020 11:08:20: #2 finished! INFO @ Tue, 14 Jul 2020 11:08:20: #2 predicted fragment length is 235 bps INFO @ Tue, 14 Jul 2020 11:08:20: #2 alternative fragment length(s) may be 235 bps INFO @ Tue, 14 Jul 2020 11:08:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8347289/SRX8347289.10_model.r WARNING @ Tue, 14 Jul 2020 11:08:20: #2 Since the d (235) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:08:20: #2 You may need to consider one of the other alternative d(s): 235 WARNING @ Tue, 14 Jul 2020 11:08:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 11:08:20: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:08:20: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 11:08:24: 7000000 INFO @ Tue, 14 Jul 2020 11:08:29: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:08:32: 8000000 INFO @ Tue, 14 Jul 2020 11:08:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8347289/SRX8347289.10_peaks.xls INFO @ Tue, 14 Jul 2020 11:08:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8347289/SRX8347289.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:08:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8347289/SRX8347289.10_summits.bed INFO @ Tue, 14 Jul 2020 11:08:33: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2322 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:08:41: 9000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 11:08:49: #1 tag size is determined as 151 bps INFO @ Tue, 14 Jul 2020 11:08:49: #1 tag size = 151 INFO @ Tue, 14 Jul 2020 11:08:49: #1 total tags in treatment: 3948049 INFO @ Tue, 14 Jul 2020 11:08:49: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:08:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 11:08:49: #1 tags after filtering in treatment: 3791171 INFO @ Tue, 14 Jul 2020 11:08:49: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 14 Jul 2020 11:08:49: #1 finished! INFO @ Tue, 14 Jul 2020 11:08:49: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:08:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:08:49: #2 number of paired peaks: 1326 INFO @ Tue, 14 Jul 2020 11:08:49: start model_add_line... INFO @ Tue, 14 Jul 2020 11:08:49: start X-correlation... INFO @ Tue, 14 Jul 2020 11:08:49: end of X-cor INFO @ Tue, 14 Jul 2020 11:08:49: #2 finished! INFO @ Tue, 14 Jul 2020 11:08:49: #2 predicted fragment length is 235 bps INFO @ Tue, 14 Jul 2020 11:08:49: #2 alternative fragment length(s) may be 235 bps INFO @ Tue, 14 Jul 2020 11:08:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8347289/SRX8347289.20_model.r WARNING @ Tue, 14 Jul 2020 11:08:49: #2 Since the d (235) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:08:49: #2 You may need to consider one of the other alternative d(s): 235 WARNING @ Tue, 14 Jul 2020 11:08:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 11:08:49: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:08:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:08:58: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:09:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8347289/SRX8347289.20_peaks.xls INFO @ Tue, 14 Jul 2020 11:09:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8347289/SRX8347289.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:09:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8347289/SRX8347289.20_summits.bed INFO @ Tue, 14 Jul 2020 11:09:02: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (953 records, 4 fields): 3 millis CompletedMACS2peakCalling