Job ID = 6627054 SRX = SRX8347276 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-14T00:41:03 prefetch.2.10.7: 1) Downloading 'SRR11795459'... 2020-07-14T00:41:03 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:14:50 prefetch.2.10.7: HTTPS download failed 2020-07-14T01:14:50 prefetch.2.10.7: 1) failed to download SRR11795459 2020-07-14T01:15:03 prefetch.2.10.7: 1) Downloading 'SRR11795459'... 2020-07-14T01:15:03 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:15:03 prefetch.2.10.7: Continue download of 'SRR11795459' from 2589723153 2020-07-14T01:15:08 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:15:08 prefetch.2.10.7: 1) 'SRR11795459' was downloaded successfully 2020-07-14T01:15:08 prefetch.2.10.7: 'SRR11795459' has 0 unresolved dependencies Read 22217415 spots for SRR11795459/SRR11795459.sra Written 22217415 spots for SRR11795459/SRR11795459.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627524 ("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: 00:53:41 22217415 reads; of these: 22217415 (100.00%) were paired; of these: 7372097 (33.18%) aligned concordantly 0 times 12051812 (54.24%) aligned concordantly exactly 1 time 2793506 (12.57%) aligned concordantly >1 times ---- 7372097 pairs aligned concordantly 0 times; of these: 1210135 (16.42%) aligned discordantly 1 time ---- 6161962 pairs aligned 0 times concordantly or discordantly; of these: 12323924 mates make up the pairs; of these: 11237212 (91.18%) aligned 0 times 432840 (3.51%) aligned exactly 1 time 653872 (5.31%) aligned >1 times 74.71% overall alignment rate Time searching: 00:53:41 Overall time: 00:53:41 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 28 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] 8505388 / 15988927 = 0.5320 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 11:21:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8347276/SRX8347276.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8347276/SRX8347276.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8347276/SRX8347276.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8347276/SRX8347276.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 11:21:57: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:21:57: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:22:05: 1000000 INFO @ Tue, 14 Jul 2020 11:22:13: 2000000 INFO @ Tue, 14 Jul 2020 11:22:20: 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 11:22:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8347276/SRX8347276.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8347276/SRX8347276.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8347276/SRX8347276.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8347276/SRX8347276.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 11:22:27: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:22:27: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:22:28: 4000000 INFO @ Tue, 14 Jul 2020 11:22:36: 1000000 INFO @ Tue, 14 Jul 2020 11:22:36: 5000000 INFO @ Tue, 14 Jul 2020 11:22:44: 2000000 INFO @ Tue, 14 Jul 2020 11:22:46: 6000000 INFO @ Tue, 14 Jul 2020 11:22:52: 3000000 INFO @ Tue, 14 Jul 2020 11:22:55: 7000000 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 11:22:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8347276/SRX8347276.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8347276/SRX8347276.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8347276/SRX8347276.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8347276/SRX8347276.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 11:22:58: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:22:58: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:23:01: 4000000 INFO @ Tue, 14 Jul 2020 11:23:04: 8000000 INFO @ Tue, 14 Jul 2020 11:23:06: 1000000 INFO @ Tue, 14 Jul 2020 11:23:09: 5000000 INFO @ Tue, 14 Jul 2020 11:23:12: 9000000 INFO @ Tue, 14 Jul 2020 11:23:16: 2000000 INFO @ Tue, 14 Jul 2020 11:23:18: 6000000 INFO @ Tue, 14 Jul 2020 11:23:21: 10000000 INFO @ Tue, 14 Jul 2020 11:23:25: 3000000 INFO @ Tue, 14 Jul 2020 11:23:27: 7000000 INFO @ Tue, 14 Jul 2020 11:23:30: 11000000 INFO @ Tue, 14 Jul 2020 11:23:34: 4000000 INFO @ Tue, 14 Jul 2020 11:23:35: 8000000 INFO @ Tue, 14 Jul 2020 11:23:39: 12000000 INFO @ Tue, 14 Jul 2020 11:23:44: 5000000 INFO @ Tue, 14 Jul 2020 11:23:44: 9000000 INFO @ Tue, 14 Jul 2020 11:23:47: 13000000 INFO @ Tue, 14 Jul 2020 11:23:52: 10000000 INFO @ Tue, 14 Jul 2020 11:23:53: 6000000 INFO @ Tue, 14 Jul 2020 11:23:56: 14000000 INFO @ Tue, 14 Jul 2020 11:24:01: 11000000 INFO @ Tue, 14 Jul 2020 11:24:02: 7000000 INFO @ Tue, 14 Jul 2020 11:24:04: 15000000 INFO @ Tue, 14 Jul 2020 11:24:10: 12000000 INFO @ Tue, 14 Jul 2020 11:24:12: 8000000 INFO @ Tue, 14 Jul 2020 11:24:13: 16000000 INFO @ Tue, 14 Jul 2020 11:24:14: #1 tag size is determined as 151 bps INFO @ Tue, 14 Jul 2020 11:24:14: #1 tag size = 151 INFO @ Tue, 14 Jul 2020 11:24:14: #1 total tags in treatment: 6789746 INFO @ Tue, 14 Jul 2020 11:24:14: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:24:14: #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 11:24:14: #1 tags after filtering in treatment: 6368235 INFO @ Tue, 14 Jul 2020 11:24:14: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 14 Jul 2020 11:24:14: #1 finished! INFO @ Tue, 14 Jul 2020 11:24:14: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:24:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:24:15: #2 number of paired peaks: 2502 INFO @ Tue, 14 Jul 2020 11:24:15: start model_add_line... INFO @ Tue, 14 Jul 2020 11:24:15: start X-correlation... INFO @ Tue, 14 Jul 2020 11:24:15: end of X-cor INFO @ Tue, 14 Jul 2020 11:24:15: #2 finished! INFO @ Tue, 14 Jul 2020 11:24:15: #2 predicted fragment length is 237 bps INFO @ Tue, 14 Jul 2020 11:24:15: #2 alternative fragment length(s) may be 237 bps INFO @ Tue, 14 Jul 2020 11:24:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8347276/SRX8347276.05_model.r WARNING @ Tue, 14 Jul 2020 11:24:15: #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 11:24:15: #2 You may need to consider one of the other alternative d(s): 237 WARNING @ Tue, 14 Jul 2020 11:24:15: #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 11:24:15: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:24:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:24:18: 13000000 INFO @ Tue, 14 Jul 2020 11:24:21: 9000000 INFO @ Tue, 14 Jul 2020 11:24:27: 14000000 INFO @ Tue, 14 Jul 2020 11:24:30: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:24:31: 10000000 INFO @ Tue, 14 Jul 2020 11:24:35: 15000000 INFO @ Tue, 14 Jul 2020 11:24:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8347276/SRX8347276.05_peaks.xls INFO @ Tue, 14 Jul 2020 11:24:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8347276/SRX8347276.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:24:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8347276/SRX8347276.05_summits.bed INFO @ Tue, 14 Jul 2020 11:24:37: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (7070 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:24:40: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 11:24:43: 16000000 INFO @ Tue, 14 Jul 2020 11:24:45: #1 tag size is determined as 151 bps INFO @ Tue, 14 Jul 2020 11:24:45: #1 tag size = 151 INFO @ Tue, 14 Jul 2020 11:24:45: #1 total tags in treatment: 6789746 INFO @ Tue, 14 Jul 2020 11:24:45: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:24:45: #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 11:24:45: #1 tags after filtering in treatment: 6368235 INFO @ Tue, 14 Jul 2020 11:24:45: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 14 Jul 2020 11:24:45: #1 finished! INFO @ Tue, 14 Jul 2020 11:24:45: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:24:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:24:46: #2 number of paired peaks: 2502 INFO @ Tue, 14 Jul 2020 11:24:46: start model_add_line... INFO @ Tue, 14 Jul 2020 11:24:46: start X-correlation... INFO @ Tue, 14 Jul 2020 11:24:46: end of X-cor INFO @ Tue, 14 Jul 2020 11:24:46: #2 finished! INFO @ Tue, 14 Jul 2020 11:24:46: #2 predicted fragment length is 237 bps INFO @ Tue, 14 Jul 2020 11:24:46: #2 alternative fragment length(s) may be 237 bps INFO @ Tue, 14 Jul 2020 11:24:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8347276/SRX8347276.10_model.r WARNING @ Tue, 14 Jul 2020 11:24:46: #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 11:24:46: #2 You may need to consider one of the other alternative d(s): 237 WARNING @ Tue, 14 Jul 2020 11:24:46: #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 11:24:46: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:24:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:24:49: 12000000 INFO @ Tue, 14 Jul 2020 11:24:58: 13000000 INFO @ Tue, 14 Jul 2020 11:25:00: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:25:07: 14000000 INFO @ Tue, 14 Jul 2020 11:25:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8347276/SRX8347276.10_peaks.xls INFO @ Tue, 14 Jul 2020 11:25:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8347276/SRX8347276.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:25:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8347276/SRX8347276.10_summits.bed INFO @ Tue, 14 Jul 2020 11:25:08: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4715 records, 4 fields): 6 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 11:25:16: 15000000 INFO @ Tue, 14 Jul 2020 11:25:24: 16000000 INFO @ Tue, 14 Jul 2020 11:25:26: #1 tag size is determined as 151 bps INFO @ Tue, 14 Jul 2020 11:25:26: #1 tag size = 151 INFO @ Tue, 14 Jul 2020 11:25:26: #1 total tags in treatment: 6789746 INFO @ Tue, 14 Jul 2020 11:25:26: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:25:26: #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 11:25:26: #1 tags after filtering in treatment: 6368235 INFO @ Tue, 14 Jul 2020 11:25:26: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 14 Jul 2020 11:25:26: #1 finished! INFO @ Tue, 14 Jul 2020 11:25:26: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:25:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:25:26: #2 number of paired peaks: 2502 INFO @ Tue, 14 Jul 2020 11:25:26: start model_add_line... INFO @ Tue, 14 Jul 2020 11:25:26: start X-correlation... INFO @ Tue, 14 Jul 2020 11:25:26: end of X-cor INFO @ Tue, 14 Jul 2020 11:25:26: #2 finished! INFO @ Tue, 14 Jul 2020 11:25:26: #2 predicted fragment length is 237 bps INFO @ Tue, 14 Jul 2020 11:25:26: #2 alternative fragment length(s) may be 237 bps INFO @ Tue, 14 Jul 2020 11:25:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8347276/SRX8347276.20_model.r WARNING @ Tue, 14 Jul 2020 11:25:26: #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 11:25:26: #2 You may need to consider one of the other alternative d(s): 237 WARNING @ Tue, 14 Jul 2020 11:25:26: #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 11:25:26: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:25:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:25:42: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:25:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8347276/SRX8347276.20_peaks.xls INFO @ Tue, 14 Jul 2020 11:25:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8347276/SRX8347276.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:25:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8347276/SRX8347276.20_summits.bed INFO @ Tue, 14 Jul 2020 11:25:49: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2727 records, 4 fields): 4 millis CompletedMACS2peakCalling