Job ID = 6627077 SRX = SRX8347286 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-14T00:46:18 prefetch.2.10.7: 1) Downloading 'SRR11795469'... 2020-07-14T00:46:18 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T00:53:03 prefetch.2.10.7: HTTPS download succeed 2020-07-14T00:53:03 prefetch.2.10.7: 1) 'SRR11795469' was downloaded successfully 2020-07-14T00:53:03 prefetch.2.10.7: 'SRR11795469' has 0 unresolved dependencies Read 17110745 spots for SRR11795469/SRR11795469.sra Written 17110745 spots for SRR11795469/SRR11795469.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627394 ("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: 00:33:58 17110745 reads; of these: 17110745 (100.00%) were paired; of these: 10005400 (58.47%) aligned concordantly 0 times 5293024 (30.93%) aligned concordantly exactly 1 time 1812321 (10.59%) aligned concordantly >1 times ---- 10005400 pairs aligned concordantly 0 times; of these: 601067 (6.01%) aligned discordantly 1 time ---- 9404333 pairs aligned 0 times concordantly or discordantly; of these: 18808666 mates make up the pairs; of these: 18136802 (96.43%) aligned 0 times 236414 (1.26%) aligned exactly 1 time 435450 (2.32%) aligned >1 times 47.00% overall alignment rate Time searching: 00:33:58 Overall time: 00:33:58 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 12 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] 4538531 / 7673514 = 0.5915 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 10:34:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8347286/SRX8347286.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8347286/SRX8347286.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8347286/SRX8347286.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8347286/SRX8347286.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 10:34:40: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:34:40: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:34:48: 1000000 INFO @ Tue, 14 Jul 2020 10:34:56: 2000000 INFO @ Tue, 14 Jul 2020 10:35:04: 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 10:35:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8347286/SRX8347286.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8347286/SRX8347286.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8347286/SRX8347286.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8347286/SRX8347286.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 10:35:10: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:35:10: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:35:12: 4000000 INFO @ Tue, 14 Jul 2020 10:35:22: 1000000 INFO @ Tue, 14 Jul 2020 10:35:23: 5000000 INFO @ Tue, 14 Jul 2020 10:35:33: 6000000 INFO @ Tue, 14 Jul 2020 10:35:35: 2000000 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 10:35:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8347286/SRX8347286.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8347286/SRX8347286.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8347286/SRX8347286.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8347286/SRX8347286.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 10:35:40: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:35:40: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:35:43: 7000000 INFO @ Tue, 14 Jul 2020 10:35:43: #1 tag size is determined as 151 bps INFO @ Tue, 14 Jul 2020 10:35:43: #1 tag size = 151 INFO @ Tue, 14 Jul 2020 10:35:43: #1 total tags in treatment: 2819497 INFO @ Tue, 14 Jul 2020 10:35:43: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:35:43: #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 10:35:44: #1 tags after filtering in treatment: 2728603 INFO @ Tue, 14 Jul 2020 10:35:44: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 14 Jul 2020 10:35:44: #1 finished! INFO @ Tue, 14 Jul 2020 10:35:44: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:35:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:35:44: #2 number of paired peaks: 1323 INFO @ Tue, 14 Jul 2020 10:35:44: start model_add_line... INFO @ Tue, 14 Jul 2020 10:35:44: start X-correlation... INFO @ Tue, 14 Jul 2020 10:35:44: end of X-cor INFO @ Tue, 14 Jul 2020 10:35:44: #2 finished! INFO @ Tue, 14 Jul 2020 10:35:44: #2 predicted fragment length is 237 bps INFO @ Tue, 14 Jul 2020 10:35:44: #2 alternative fragment length(s) may be 237 bps INFO @ Tue, 14 Jul 2020 10:35:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8347286/SRX8347286.05_model.r WARNING @ Tue, 14 Jul 2020 10:35:44: #2 Since the d (237) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:35:44: #2 You may need to consider one of the other alternative d(s): 237 WARNING @ Tue, 14 Jul 2020 10:35:44: #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 10:35:44: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:35:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:35:47: 3000000 INFO @ Tue, 14 Jul 2020 10:35:50: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:35:51: 1000000 INFO @ Tue, 14 Jul 2020 10:35:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8347286/SRX8347286.05_peaks.xls INFO @ Tue, 14 Jul 2020 10:35:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8347286/SRX8347286.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:35:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8347286/SRX8347286.05_summits.bed INFO @ Tue, 14 Jul 2020 10:35:53: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3022 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:35:58: 4000000 INFO @ Tue, 14 Jul 2020 10:36:02: 2000000 INFO @ Tue, 14 Jul 2020 10:36:11: 5000000 INFO @ Tue, 14 Jul 2020 10:36:12: 3000000 INFO @ Tue, 14 Jul 2020 10:36:22: 4000000 INFO @ Tue, 14 Jul 2020 10:36:23: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 10:36:33: 5000000 INFO @ Tue, 14 Jul 2020 10:36:35: 7000000 INFO @ Tue, 14 Jul 2020 10:36:35: #1 tag size is determined as 151 bps INFO @ Tue, 14 Jul 2020 10:36:35: #1 tag size = 151 INFO @ Tue, 14 Jul 2020 10:36:35: #1 total tags in treatment: 2819497 INFO @ Tue, 14 Jul 2020 10:36:35: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:36:35: #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 10:36:35: #1 tags after filtering in treatment: 2728603 INFO @ Tue, 14 Jul 2020 10:36:35: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 14 Jul 2020 10:36:35: #1 finished! INFO @ Tue, 14 Jul 2020 10:36:35: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:36:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:36:35: #2 number of paired peaks: 1323 INFO @ Tue, 14 Jul 2020 10:36:35: start model_add_line... INFO @ Tue, 14 Jul 2020 10:36:35: start X-correlation... INFO @ Tue, 14 Jul 2020 10:36:35: end of X-cor INFO @ Tue, 14 Jul 2020 10:36:35: #2 finished! INFO @ Tue, 14 Jul 2020 10:36:35: #2 predicted fragment length is 237 bps INFO @ Tue, 14 Jul 2020 10:36:35: #2 alternative fragment length(s) may be 237 bps INFO @ Tue, 14 Jul 2020 10:36:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8347286/SRX8347286.10_model.r WARNING @ Tue, 14 Jul 2020 10:36:35: #2 Since the d (237) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:36:35: #2 You may need to consider one of the other alternative d(s): 237 WARNING @ Tue, 14 Jul 2020 10:36:35: #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 10:36:35: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:36:35: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 10:36:41: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:36:42: 6000000 INFO @ Tue, 14 Jul 2020 10:36:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8347286/SRX8347286.10_peaks.xls INFO @ Tue, 14 Jul 2020 10:36:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8347286/SRX8347286.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:36:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8347286/SRX8347286.10_summits.bed INFO @ Tue, 14 Jul 2020 10:36:45: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1640 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:36:51: 7000000 INFO @ Tue, 14 Jul 2020 10:36:51: #1 tag size is determined as 151 bps INFO @ Tue, 14 Jul 2020 10:36:51: #1 tag size = 151 INFO @ Tue, 14 Jul 2020 10:36:51: #1 total tags in treatment: 2819497 INFO @ Tue, 14 Jul 2020 10:36:51: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:36:51: #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 10:36:52: #1 tags after filtering in treatment: 2728603 INFO @ Tue, 14 Jul 2020 10:36:52: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 14 Jul 2020 10:36:52: #1 finished! INFO @ Tue, 14 Jul 2020 10:36:52: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:36:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:36:52: #2 number of paired peaks: 1323 INFO @ Tue, 14 Jul 2020 10:36:52: start model_add_line... INFO @ Tue, 14 Jul 2020 10:36:52: start X-correlation... INFO @ Tue, 14 Jul 2020 10:36:52: end of X-cor INFO @ Tue, 14 Jul 2020 10:36:52: #2 finished! INFO @ Tue, 14 Jul 2020 10:36:52: #2 predicted fragment length is 237 bps INFO @ Tue, 14 Jul 2020 10:36:52: #2 alternative fragment length(s) may be 237 bps INFO @ Tue, 14 Jul 2020 10:36:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8347286/SRX8347286.20_model.r WARNING @ Tue, 14 Jul 2020 10:36:52: #2 Since the d (237) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:36:52: #2 You may need to consider one of the other alternative d(s): 237 WARNING @ Tue, 14 Jul 2020 10:36:52: #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 10:36:52: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:36:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:36:58: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:37:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8347286/SRX8347286.20_peaks.xls INFO @ Tue, 14 Jul 2020 10:37:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8347286/SRX8347286.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:37:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8347286/SRX8347286.20_summits.bed INFO @ Tue, 14 Jul 2020 10:37:01: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (581 records, 4 fields): 2 millis CompletedMACS2peakCalling