Job ID = 6498684 SRX = SRX699109 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T23:47:52 prefetch.2.10.7: 1) Downloading 'SRR1573149'... 2020-06-25T23:47:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:51:43 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:51:43 prefetch.2.10.7: 1) 'SRR1573149' was downloaded successfully Read 7045596 spots for SRR1573149/SRR1573149.sra Written 7045596 spots for SRR1573149/SRR1573149.sra 2020-06-25T23:52:40 prefetch.2.10.7: 1) Downloading 'SRR1573150'... 2020-06-25T23:52:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:55:24 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:55:24 prefetch.2.10.7: 1) 'SRR1573150' was downloaded successfully Read 7159774 spots for SRR1573150/SRR1573150.sra Written 7159774 spots for SRR1573150/SRR1573150.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: 00:50:59 14205370 reads; of these: 14205370 (100.00%) were paired; of these: 824736 (5.81%) aligned concordantly 0 times 8747517 (61.58%) aligned concordantly exactly 1 time 4633117 (32.62%) aligned concordantly >1 times ---- 824736 pairs aligned concordantly 0 times; of these: 109721 (13.30%) aligned discordantly 1 time ---- 715015 pairs aligned 0 times concordantly or discordantly; of these: 1430030 mates make up the pairs; of these: 744605 (52.07%) aligned 0 times 310391 (21.71%) aligned exactly 1 time 375034 (26.23%) aligned >1 times 97.38% overall alignment rate Time searching: 00:50:59 Overall time: 00:50:59 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] 2012428 / 13434864 = 0.1498 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 09:58:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX699109/SRX699109.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX699109/SRX699109.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX699109/SRX699109.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX699109/SRX699109.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 09:58:42: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:58:42: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:58:48: 1000000 INFO @ Fri, 26 Jun 2020 09:58:55: 2000000 INFO @ Fri, 26 Jun 2020 09:59:02: 3000000 INFO @ Fri, 26 Jun 2020 09:59:08: 4000000 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 09:59:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX699109/SRX699109.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX699109/SRX699109.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX699109/SRX699109.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX699109/SRX699109.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 09:59:12: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:59:12: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:59:15: 5000000 INFO @ Fri, 26 Jun 2020 09:59:18: 1000000 INFO @ Fri, 26 Jun 2020 09:59:22: 6000000 INFO @ Fri, 26 Jun 2020 09:59:25: 2000000 INFO @ Fri, 26 Jun 2020 09:59:29: 7000000 INFO @ Fri, 26 Jun 2020 09:59:32: 3000000 INFO @ Fri, 26 Jun 2020 09:59:36: 8000000 INFO @ Fri, 26 Jun 2020 09:59:39: 4000000 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 09:59:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX699109/SRX699109.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX699109/SRX699109.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX699109/SRX699109.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX699109/SRX699109.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 09:59:42: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:59:42: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:59:43: 9000000 INFO @ Fri, 26 Jun 2020 09:59:46: 5000000 INFO @ Fri, 26 Jun 2020 09:59:49: 1000000 INFO @ Fri, 26 Jun 2020 09:59:50: 10000000 INFO @ Fri, 26 Jun 2020 09:59:53: 6000000 INFO @ Fri, 26 Jun 2020 09:59:56: 2000000 INFO @ Fri, 26 Jun 2020 09:59:57: 11000000 INFO @ Fri, 26 Jun 2020 10:00:00: 7000000 INFO @ Fri, 26 Jun 2020 10:00:03: 3000000 INFO @ Fri, 26 Jun 2020 10:00:04: 12000000 INFO @ Fri, 26 Jun 2020 10:00:06: 8000000 INFO @ Fri, 26 Jun 2020 10:00:09: 4000000 INFO @ Fri, 26 Jun 2020 10:00:11: 13000000 INFO @ Fri, 26 Jun 2020 10:00:13: 9000000 INFO @ Fri, 26 Jun 2020 10:00:16: 5000000 INFO @ Fri, 26 Jun 2020 10:00:18: 14000000 INFO @ Fri, 26 Jun 2020 10:00:20: 10000000 INFO @ Fri, 26 Jun 2020 10:00:23: 6000000 INFO @ Fri, 26 Jun 2020 10:00:25: 15000000 INFO @ Fri, 26 Jun 2020 10:00:26: 11000000 INFO @ Fri, 26 Jun 2020 10:00:29: 7000000 INFO @ Fri, 26 Jun 2020 10:00:32: 16000000 INFO @ Fri, 26 Jun 2020 10:00:33: 12000000 INFO @ Fri, 26 Jun 2020 10:00:36: 8000000 INFO @ Fri, 26 Jun 2020 10:00:39: 17000000 INFO @ Fri, 26 Jun 2020 10:00:40: 13000000 INFO @ Fri, 26 Jun 2020 10:00:43: 9000000 INFO @ Fri, 26 Jun 2020 10:00:45: 18000000 INFO @ Fri, 26 Jun 2020 10:00:46: 14000000 INFO @ Fri, 26 Jun 2020 10:00:49: 10000000 INFO @ Fri, 26 Jun 2020 10:00:52: 19000000 INFO @ Fri, 26 Jun 2020 10:00:53: 15000000 INFO @ Fri, 26 Jun 2020 10:00:56: 11000000 INFO @ Fri, 26 Jun 2020 10:00:59: 20000000 INFO @ Fri, 26 Jun 2020 10:01:00: 16000000 INFO @ Fri, 26 Jun 2020 10:01:02: 12000000 INFO @ Fri, 26 Jun 2020 10:01:06: 21000000 INFO @ Fri, 26 Jun 2020 10:01:06: 17000000 INFO @ Fri, 26 Jun 2020 10:01:09: 13000000 INFO @ Fri, 26 Jun 2020 10:01:13: 22000000 INFO @ Fri, 26 Jun 2020 10:01:13: 18000000 INFO @ Fri, 26 Jun 2020 10:01:16: 14000000 INFO @ Fri, 26 Jun 2020 10:01:19: 23000000 INFO @ Fri, 26 Jun 2020 10:01:20: 19000000 INFO @ Fri, 26 Jun 2020 10:01:22: 15000000 INFO @ Fri, 26 Jun 2020 10:01:24: #1 tag size is determined as 101 bps INFO @ Fri, 26 Jun 2020 10:01:24: #1 tag size = 101 INFO @ Fri, 26 Jun 2020 10:01:24: #1 total tags in treatment: 11374774 INFO @ Fri, 26 Jun 2020 10:01:24: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 10:01:24: #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 10:01:24: #1 tags after filtering in treatment: 9932907 INFO @ Fri, 26 Jun 2020 10:01:24: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 26 Jun 2020 10:01:24: #1 finished! INFO @ Fri, 26 Jun 2020 10:01:24: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 10:01:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 10:01:25: #2 number of paired peaks: 1155 INFO @ Fri, 26 Jun 2020 10:01:25: start model_add_line... INFO @ Fri, 26 Jun 2020 10:01:25: start X-correlation... INFO @ Fri, 26 Jun 2020 10:01:25: end of X-cor INFO @ Fri, 26 Jun 2020 10:01:25: #2 finished! INFO @ Fri, 26 Jun 2020 10:01:25: #2 predicted fragment length is 164 bps INFO @ Fri, 26 Jun 2020 10:01:25: #2 alternative fragment length(s) may be 164 bps INFO @ Fri, 26 Jun 2020 10:01:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX699109/SRX699109.05_model.r WARNING @ Fri, 26 Jun 2020 10:01:25: #2 Since the d (164) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 10:01:25: #2 You may need to consider one of the other alternative d(s): 164 WARNING @ Fri, 26 Jun 2020 10:01:25: #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 10:01:25: #3 Call peaks... INFO @ Fri, 26 Jun 2020 10:01:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 10:01:26: 20000000 INFO @ Fri, 26 Jun 2020 10:01:29: 16000000 INFO @ Fri, 26 Jun 2020 10:01:33: 21000000 INFO @ Fri, 26 Jun 2020 10:01:35: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 10:01:40: 22000000 INFO @ Fri, 26 Jun 2020 10:01:42: 18000000 INFO @ Fri, 26 Jun 2020 10:01:47: 23000000 INFO @ Fri, 26 Jun 2020 10:01:47: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 10:01:49: 19000000 INFO @ Fri, 26 Jun 2020 10:01:51: #1 tag size is determined as 101 bps INFO @ Fri, 26 Jun 2020 10:01:51: #1 tag size = 101 INFO @ Fri, 26 Jun 2020 10:01:51: #1 total tags in treatment: 11374774 INFO @ Fri, 26 Jun 2020 10:01:51: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 10:01:51: #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 10:01:51: #1 tags after filtering in treatment: 9932907 INFO @ Fri, 26 Jun 2020 10:01:51: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 26 Jun 2020 10:01:51: #1 finished! INFO @ Fri, 26 Jun 2020 10:01:51: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 10:01:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 10:01:52: #2 number of paired peaks: 1155 INFO @ Fri, 26 Jun 2020 10:01:52: start model_add_line... INFO @ Fri, 26 Jun 2020 10:01:52: start X-correlation... INFO @ Fri, 26 Jun 2020 10:01:52: end of X-cor INFO @ Fri, 26 Jun 2020 10:01:52: #2 finished! INFO @ Fri, 26 Jun 2020 10:01:52: #2 predicted fragment length is 164 bps INFO @ Fri, 26 Jun 2020 10:01:52: #2 alternative fragment length(s) may be 164 bps INFO @ Fri, 26 Jun 2020 10:01:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX699109/SRX699109.10_model.r WARNING @ Fri, 26 Jun 2020 10:01:52: #2 Since the d (164) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 10:01:52: #2 You may need to consider one of the other alternative d(s): 164 WARNING @ Fri, 26 Jun 2020 10:01:52: #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 10:01:52: #3 Call peaks... INFO @ Fri, 26 Jun 2020 10:01:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 10:01:55: 20000000 INFO @ Fri, 26 Jun 2020 10:01:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX699109/SRX699109.05_peaks.xls INFO @ Fri, 26 Jun 2020 10:02:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX699109/SRX699109.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 10:02:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX699109/SRX699109.05_summits.bed INFO @ Fri, 26 Jun 2020 10:02:00: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (20951 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 10:02:01: 21000000 INFO @ Fri, 26 Jun 2020 10:02:08: 22000000 INFO @ Fri, 26 Jun 2020 10:02:14: 23000000 INFO @ Fri, 26 Jun 2020 10:02:15: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 10:02:18: #1 tag size is determined as 101 bps INFO @ Fri, 26 Jun 2020 10:02:18: #1 tag size = 101 INFO @ Fri, 26 Jun 2020 10:02:18: #1 total tags in treatment: 11374774 INFO @ Fri, 26 Jun 2020 10:02:18: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 10:02:18: #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 10:02:18: #1 tags after filtering in treatment: 9932907 INFO @ Fri, 26 Jun 2020 10:02:18: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 26 Jun 2020 10:02:18: #1 finished! INFO @ Fri, 26 Jun 2020 10:02:18: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 10:02:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 10:02:19: #2 number of paired peaks: 1155 INFO @ Fri, 26 Jun 2020 10:02:19: start model_add_line... INFO @ Fri, 26 Jun 2020 10:02:19: start X-correlation... INFO @ Fri, 26 Jun 2020 10:02:19: end of X-cor INFO @ Fri, 26 Jun 2020 10:02:19: #2 finished! INFO @ Fri, 26 Jun 2020 10:02:19: #2 predicted fragment length is 164 bps INFO @ Fri, 26 Jun 2020 10:02:19: #2 alternative fragment length(s) may be 164 bps INFO @ Fri, 26 Jun 2020 10:02:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX699109/SRX699109.20_model.r WARNING @ Fri, 26 Jun 2020 10:02:19: #2 Since the d (164) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 10:02:19: #2 You may need to consider one of the other alternative d(s): 164 WARNING @ Fri, 26 Jun 2020 10:02:19: #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 10:02:19: #3 Call peaks... INFO @ Fri, 26 Jun 2020 10:02:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 10:02:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX699109/SRX699109.10_peaks.xls INFO @ Fri, 26 Jun 2020 10:02:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX699109/SRX699109.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 10:02:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX699109/SRX699109.10_summits.bed INFO @ Fri, 26 Jun 2020 10:02:27: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9694 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 10:02:42: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 10:02:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX699109/SRX699109.20_peaks.xls INFO @ Fri, 26 Jun 2020 10:02:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX699109/SRX699109.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 10:02:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX699109/SRX699109.20_summits.bed INFO @ Fri, 26 Jun 2020 10:02:54: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3028 records, 4 fields): 5 millis CompletedMACS2peakCalling