Job ID = 6498687 SRX = SRX699112 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T23:53:37 prefetch.2.10.7: 1) Downloading 'SRR1573155'... 2020-06-25T23:53:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:55:38 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:55:39 prefetch.2.10.7: 'SRR1573155' is valid 2020-06-25T23:55:39 prefetch.2.10.7: 1) 'SRR1573155' was downloaded successfully Read 4017365 spots for SRR1573155/SRR1573155.sra Written 4017365 spots for SRR1573155/SRR1573155.sra 2020-06-25T23:56:18 prefetch.2.10.7: 1) Downloading 'SRR1573156'... 2020-06-25T23:56:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:57:51 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:57:52 prefetch.2.10.7: 'SRR1573156' is valid 2020-06-25T23:57:52 prefetch.2.10.7: 1) 'SRR1573156' was downloaded successfully Read 4062801 spots for SRR1573156/SRR1573156.sra Written 4062801 spots for SRR1573156/SRR1573156.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:12:13 8080166 reads; of these: 8080166 (100.00%) were paired; of these: 244833 (3.03%) aligned concordantly 0 times 7105424 (87.94%) aligned concordantly exactly 1 time 729909 (9.03%) aligned concordantly >1 times ---- 244833 pairs aligned concordantly 0 times; of these: 22200 (9.07%) aligned discordantly 1 time ---- 222633 pairs aligned 0 times concordantly or discordantly; of these: 445266 mates make up the pairs; of these: 245390 (55.11%) aligned 0 times 135881 (30.52%) aligned exactly 1 time 63995 (14.37%) aligned >1 times 98.48% overall alignment rate Time searching: 00:12:14 Overall time: 00:12:14 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 8 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] 556586 / 7854443 = 0.0709 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 @ Fri, 26 Jun 2020 09:17:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX699112/SRX699112.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX699112/SRX699112.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX699112/SRX699112.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX699112/SRX699112.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 @ Fri, 26 Jun 2020 09:17:14: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:17:14: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:17:23: 1000000 INFO @ Fri, 26 Jun 2020 09:17:32: 2000000 INFO @ Fri, 26 Jun 2020 09:17:41: 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 @ Fri, 26 Jun 2020 09:17:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX699112/SRX699112.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX699112/SRX699112.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX699112/SRX699112.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX699112/SRX699112.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 @ Fri, 26 Jun 2020 09:17:44: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:17:44: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:17:50: 4000000 INFO @ Fri, 26 Jun 2020 09:17:53: 1000000 INFO @ Fri, 26 Jun 2020 09:18:01: 5000000 INFO @ Fri, 26 Jun 2020 09:18:02: 2000000 INFO @ Fri, 26 Jun 2020 09:18:10: 3000000 INFO @ Fri, 26 Jun 2020 09:18:11: 6000000 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 @ Fri, 26 Jun 2020 09:18:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX699112/SRX699112.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX699112/SRX699112.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX699112/SRX699112.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX699112/SRX699112.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 @ Fri, 26 Jun 2020 09:18:14: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:18:14: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:18:19: 4000000 INFO @ Fri, 26 Jun 2020 09:18:21: 7000000 INFO @ Fri, 26 Jun 2020 09:18:24: 1000000 INFO @ Fri, 26 Jun 2020 09:18:28: 5000000 INFO @ Fri, 26 Jun 2020 09:18:32: 8000000 INFO @ Fri, 26 Jun 2020 09:18:35: 2000000 INFO @ Fri, 26 Jun 2020 09:18:38: 6000000 INFO @ Fri, 26 Jun 2020 09:18:42: 9000000 INFO @ Fri, 26 Jun 2020 09:18:44: 3000000 INFO @ Fri, 26 Jun 2020 09:18:47: 7000000 INFO @ Fri, 26 Jun 2020 09:18:53: 10000000 INFO @ Fri, 26 Jun 2020 09:18:54: 4000000 INFO @ Fri, 26 Jun 2020 09:18:56: 8000000 INFO @ Fri, 26 Jun 2020 09:19:04: 11000000 INFO @ Fri, 26 Jun 2020 09:19:04: 5000000 INFO @ Fri, 26 Jun 2020 09:19:05: 9000000 INFO @ Fri, 26 Jun 2020 09:19:13: 6000000 INFO @ Fri, 26 Jun 2020 09:19:14: 10000000 INFO @ Fri, 26 Jun 2020 09:19:14: 12000000 INFO @ Fri, 26 Jun 2020 09:19:23: 11000000 INFO @ Fri, 26 Jun 2020 09:19:23: 7000000 INFO @ Fri, 26 Jun 2020 09:19:25: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:19:32: 12000000 INFO @ Fri, 26 Jun 2020 09:19:33: 8000000 INFO @ Fri, 26 Jun 2020 09:19:35: 14000000 INFO @ Fri, 26 Jun 2020 09:19:41: 13000000 INFO @ Fri, 26 Jun 2020 09:19:43: 9000000 INFO @ Fri, 26 Jun 2020 09:19:43: #1 tag size is determined as 101 bps INFO @ Fri, 26 Jun 2020 09:19:43: #1 tag size = 101 INFO @ Fri, 26 Jun 2020 09:19:43: #1 total tags in treatment: 7279616 INFO @ Fri, 26 Jun 2020 09:19:43: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:19:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:19:43: #1 tags after filtering in treatment: 6663683 INFO @ Fri, 26 Jun 2020 09:19:43: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 26 Jun 2020 09:19:43: #1 finished! INFO @ Fri, 26 Jun 2020 09:19:43: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:19:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:19:44: #2 number of paired peaks: 4337 INFO @ Fri, 26 Jun 2020 09:19:44: start model_add_line... INFO @ Fri, 26 Jun 2020 09:19:44: start X-correlation... INFO @ Fri, 26 Jun 2020 09:19:44: end of X-cor INFO @ Fri, 26 Jun 2020 09:19:44: #2 finished! INFO @ Fri, 26 Jun 2020 09:19:44: #2 predicted fragment length is 192 bps INFO @ Fri, 26 Jun 2020 09:19:44: #2 alternative fragment length(s) may be 192 bps INFO @ Fri, 26 Jun 2020 09:19:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX699112/SRX699112.05_model.r WARNING @ Fri, 26 Jun 2020 09:19:44: #2 Since the d (192) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:19:44: #2 You may need to consider one of the other alternative d(s): 192 WARNING @ Fri, 26 Jun 2020 09:19:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 09:19:44: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:19:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:19:50: 14000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 09:19:52: 10000000 INFO @ Fri, 26 Jun 2020 09:19:57: #1 tag size is determined as 101 bps INFO @ Fri, 26 Jun 2020 09:19:57: #1 tag size = 101 INFO @ Fri, 26 Jun 2020 09:19:57: #1 total tags in treatment: 7279616 INFO @ Fri, 26 Jun 2020 09:19:57: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:19:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:19:57: #1 tags after filtering in treatment: 6663683 INFO @ Fri, 26 Jun 2020 09:19:57: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 26 Jun 2020 09:19:57: #1 finished! INFO @ Fri, 26 Jun 2020 09:19:57: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:19:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:19:58: #2 number of paired peaks: 4337 INFO @ Fri, 26 Jun 2020 09:19:58: start model_add_line... INFO @ Fri, 26 Jun 2020 09:19:58: start X-correlation... INFO @ Fri, 26 Jun 2020 09:19:58: end of X-cor INFO @ Fri, 26 Jun 2020 09:19:58: #2 finished! INFO @ Fri, 26 Jun 2020 09:19:58: #2 predicted fragment length is 192 bps INFO @ Fri, 26 Jun 2020 09:19:58: #2 alternative fragment length(s) may be 192 bps INFO @ Fri, 26 Jun 2020 09:19:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX699112/SRX699112.10_model.r WARNING @ Fri, 26 Jun 2020 09:19:58: #2 Since the d (192) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:19:58: #2 You may need to consider one of the other alternative d(s): 192 WARNING @ Fri, 26 Jun 2020 09:19:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 09:19:58: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:19:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:20:02: 11000000 INFO @ Fri, 26 Jun 2020 09:20:02: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:20:10: 12000000 INFO @ Fri, 26 Jun 2020 09:20:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX699112/SRX699112.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:20:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX699112/SRX699112.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:20:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX699112/SRX699112.05_summits.bed INFO @ Fri, 26 Jun 2020 09:20:11: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (12883 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:20:15: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:20:19: 13000000 INFO @ Fri, 26 Jun 2020 09:20:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX699112/SRX699112.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:20:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX699112/SRX699112.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:20:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX699112/SRX699112.10_summits.bed INFO @ Fri, 26 Jun 2020 09:20:24: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7095 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:20:27: 14000000 INFO @ Fri, 26 Jun 2020 09:20:34: #1 tag size is determined as 101 bps INFO @ Fri, 26 Jun 2020 09:20:34: #1 tag size = 101 INFO @ Fri, 26 Jun 2020 09:20:34: #1 total tags in treatment: 7279616 INFO @ Fri, 26 Jun 2020 09:20:34: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:20:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:20:34: #1 tags after filtering in treatment: 6663683 INFO @ Fri, 26 Jun 2020 09:20:34: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 26 Jun 2020 09:20:34: #1 finished! INFO @ Fri, 26 Jun 2020 09:20:34: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:20:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:20:35: #2 number of paired peaks: 4337 INFO @ Fri, 26 Jun 2020 09:20:35: start model_add_line... INFO @ Fri, 26 Jun 2020 09:20:35: start X-correlation... INFO @ Fri, 26 Jun 2020 09:20:35: end of X-cor INFO @ Fri, 26 Jun 2020 09:20:35: #2 finished! INFO @ Fri, 26 Jun 2020 09:20:35: #2 predicted fragment length is 192 bps INFO @ Fri, 26 Jun 2020 09:20:35: #2 alternative fragment length(s) may be 192 bps INFO @ Fri, 26 Jun 2020 09:20:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX699112/SRX699112.20_model.r WARNING @ Fri, 26 Jun 2020 09:20:35: #2 Since the d (192) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:20:35: #2 You may need to consider one of the other alternative d(s): 192 WARNING @ Fri, 26 Jun 2020 09:20:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 09:20:35: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:20:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:20:53: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:21:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX699112/SRX699112.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:21:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX699112/SRX699112.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:21:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX699112/SRX699112.20_summits.bed INFO @ Fri, 26 Jun 2020 09:21:03: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (3254 records, 4 fields): 5 millis CompletedMACS2peakCalling