Job ID = 6627023 SRX = SRX8325349 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-14T00:27:04 prefetch.2.10.7: 1) Downloading 'SRR11772155'... 2020-07-14T00:27:04 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T00:33:18 prefetch.2.10.7: HTTPS download succeed 2020-07-14T00:33:18 prefetch.2.10.7: 1) 'SRR11772155' was downloaded successfully 2020-07-14T00:33:18 prefetch.2.10.7: 'SRR11772155' has 0 unresolved dependencies Read 11040889 spots for SRR11772155/SRR11772155.sra Written 11040889 spots for SRR11772155/SRR11772155.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627386 ("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: 00:51:18 11040889 reads; of these: 11040889 (100.00%) were paired; of these: 2941476 (26.64%) aligned concordantly 0 times 4286416 (38.82%) aligned concordantly exactly 1 time 3812997 (34.54%) aligned concordantly >1 times ---- 2941476 pairs aligned concordantly 0 times; of these: 591045 (20.09%) aligned discordantly 1 time ---- 2350431 pairs aligned 0 times concordantly or discordantly; of these: 4700862 mates make up the pairs; of these: 2413082 (51.33%) aligned 0 times 943847 (20.08%) aligned exactly 1 time 1343933 (28.59%) aligned >1 times 89.07% overall alignment rate Time searching: 00:51:18 Overall time: 00:51:18 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 16 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] 5406692 / 8170300 = 0.6617 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 10:33:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8325349/SRX8325349.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8325349/SRX8325349.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8325349/SRX8325349.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8325349/SRX8325349.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 10:33:27: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:33:27: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:33:37: 1000000 INFO @ Tue, 14 Jul 2020 10:33:48: 2000000 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 10:33:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8325349/SRX8325349.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8325349/SRX8325349.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8325349/SRX8325349.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8325349/SRX8325349.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 10:33:57: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:33:57: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:33:59: 3000000 INFO @ Tue, 14 Jul 2020 10:34:07: 1000000 INFO @ Tue, 14 Jul 2020 10:34:10: 4000000 INFO @ Tue, 14 Jul 2020 10:34:18: 2000000 INFO @ Tue, 14 Jul 2020 10:34:22: 5000000 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 10:34:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8325349/SRX8325349.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8325349/SRX8325349.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8325349/SRX8325349.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8325349/SRX8325349.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 10:34:27: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:34:27: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:34:28: 3000000 INFO @ Tue, 14 Jul 2020 10:34:33: 6000000 INFO @ Tue, 14 Jul 2020 10:34:39: 1000000 INFO @ Tue, 14 Jul 2020 10:34:40: 4000000 INFO @ Tue, 14 Jul 2020 10:34:45: 7000000 INFO @ Tue, 14 Jul 2020 10:34:52: 2000000 INFO @ Tue, 14 Jul 2020 10:34:52: 5000000 INFO @ Tue, 14 Jul 2020 10:34:57: 8000000 INFO @ Tue, 14 Jul 2020 10:35:04: 6000000 INFO @ Tue, 14 Jul 2020 10:35:04: 3000000 INFO @ Tue, 14 Jul 2020 10:35:06: #1 tag size is determined as 150 bps INFO @ Tue, 14 Jul 2020 10:35:06: #1 tag size = 150 INFO @ Tue, 14 Jul 2020 10:35:06: #1 total tags in treatment: 3041404 INFO @ Tue, 14 Jul 2020 10:35:06: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:35:06: #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 10:35:06: #1 tags after filtering in treatment: 2281975 INFO @ Tue, 14 Jul 2020 10:35:06: #1 Redundant rate of treatment: 0.25 INFO @ Tue, 14 Jul 2020 10:35:06: #1 finished! INFO @ Tue, 14 Jul 2020 10:35:06: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:35:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:35:07: #2 number of paired peaks: 2196 INFO @ Tue, 14 Jul 2020 10:35:07: start model_add_line... INFO @ Tue, 14 Jul 2020 10:35:07: start X-correlation... INFO @ Tue, 14 Jul 2020 10:35:07: end of X-cor INFO @ Tue, 14 Jul 2020 10:35:07: #2 finished! INFO @ Tue, 14 Jul 2020 10:35:07: #2 predicted fragment length is 202 bps INFO @ Tue, 14 Jul 2020 10:35:07: #2 alternative fragment length(s) may be 202 bps INFO @ Tue, 14 Jul 2020 10:35:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8325349/SRX8325349.05_model.r WARNING @ Tue, 14 Jul 2020 10:35:07: #2 Since the d (202) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:35:07: #2 You may need to consider one of the other alternative d(s): 202 WARNING @ Tue, 14 Jul 2020 10:35:07: #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 10:35:07: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:35:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:35:12: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:35:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8325349/SRX8325349.05_peaks.xls INFO @ Tue, 14 Jul 2020 10:35:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8325349/SRX8325349.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:35:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8325349/SRX8325349.05_summits.bed INFO @ Tue, 14 Jul 2020 10:35:15: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5037 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:35:16: 7000000 INFO @ Tue, 14 Jul 2020 10:35:16: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 10:35:27: 8000000 INFO @ Tue, 14 Jul 2020 10:35:28: 5000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 10:35:36: #1 tag size is determined as 150 bps INFO @ Tue, 14 Jul 2020 10:35:36: #1 tag size = 150 INFO @ Tue, 14 Jul 2020 10:35:36: #1 total tags in treatment: 3041404 INFO @ Tue, 14 Jul 2020 10:35:36: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:35:36: #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 10:35:36: #1 tags after filtering in treatment: 2281975 INFO @ Tue, 14 Jul 2020 10:35:36: #1 Redundant rate of treatment: 0.25 INFO @ Tue, 14 Jul 2020 10:35:36: #1 finished! INFO @ Tue, 14 Jul 2020 10:35:36: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:35:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:35:37: #2 number of paired peaks: 2196 INFO @ Tue, 14 Jul 2020 10:35:37: start model_add_line... INFO @ Tue, 14 Jul 2020 10:35:37: start X-correlation... INFO @ Tue, 14 Jul 2020 10:35:37: end of X-cor INFO @ Tue, 14 Jul 2020 10:35:37: #2 finished! INFO @ Tue, 14 Jul 2020 10:35:37: #2 predicted fragment length is 202 bps INFO @ Tue, 14 Jul 2020 10:35:37: #2 alternative fragment length(s) may be 202 bps INFO @ Tue, 14 Jul 2020 10:35:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8325349/SRX8325349.10_model.r WARNING @ Tue, 14 Jul 2020 10:35:37: #2 Since the d (202) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:35:37: #2 You may need to consider one of the other alternative d(s): 202 WARNING @ Tue, 14 Jul 2020 10:35:37: #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 10:35:37: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:35:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:35:39: 6000000 INFO @ Tue, 14 Jul 2020 10:35:42: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:35:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8325349/SRX8325349.10_peaks.xls INFO @ Tue, 14 Jul 2020 10:35:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8325349/SRX8325349.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:35:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8325349/SRX8325349.10_summits.bed INFO @ Tue, 14 Jul 2020 10:35:45: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2268 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:35:50: 7000000 INFO @ Tue, 14 Jul 2020 10:36:01: 8000000 INFO @ Tue, 14 Jul 2020 10:36:10: #1 tag size is determined as 150 bps INFO @ Tue, 14 Jul 2020 10:36:10: #1 tag size = 150 INFO @ Tue, 14 Jul 2020 10:36:10: #1 total tags in treatment: 3041404 INFO @ Tue, 14 Jul 2020 10:36:10: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:36:10: #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 10:36:10: #1 tags after filtering in treatment: 2281975 INFO @ Tue, 14 Jul 2020 10:36:10: #1 Redundant rate of treatment: 0.25 INFO @ Tue, 14 Jul 2020 10:36:10: #1 finished! INFO @ Tue, 14 Jul 2020 10:36:10: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:36:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:36:10: #2 number of paired peaks: 2196 INFO @ Tue, 14 Jul 2020 10:36:10: start model_add_line... INFO @ Tue, 14 Jul 2020 10:36:10: start X-correlation... INFO @ Tue, 14 Jul 2020 10:36:10: end of X-cor INFO @ Tue, 14 Jul 2020 10:36:10: #2 finished! INFO @ Tue, 14 Jul 2020 10:36:10: #2 predicted fragment length is 202 bps INFO @ Tue, 14 Jul 2020 10:36:10: #2 alternative fragment length(s) may be 202 bps INFO @ Tue, 14 Jul 2020 10:36:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8325349/SRX8325349.20_model.r WARNING @ Tue, 14 Jul 2020 10:36:10: #2 Since the d (202) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:36:10: #2 You may need to consider one of the other alternative d(s): 202 WARNING @ Tue, 14 Jul 2020 10:36:10: #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 10:36:10: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:36:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:36:15: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:36:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8325349/SRX8325349.20_peaks.xls INFO @ Tue, 14 Jul 2020 10:36:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8325349/SRX8325349.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:36:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8325349/SRX8325349.20_summits.bed INFO @ Tue, 14 Jul 2020 10:36:18: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (804 records, 4 fields): 3 millis CompletedMACS2peakCalling