Job ID = 6626571 SRX = SRX7224573 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 19053440 spots for SRR10541131/SRR10541131.sra Written 19053440 spots for SRR10541131/SRR10541131.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626785 ("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: 00:39:09 19053440 reads; of these: 19053440 (100.00%) were paired; of these: 5715595 (30.00%) aligned concordantly 0 times 12092368 (63.47%) aligned concordantly exactly 1 time 1245477 (6.54%) aligned concordantly >1 times ---- 5715595 pairs aligned concordantly 0 times; of these: 3531220 (61.78%) aligned discordantly 1 time ---- 2184375 pairs aligned 0 times concordantly or discordantly; of these: 4368750 mates make up the pairs; of these: 3228547 (73.90%) aligned 0 times 388681 (8.90%) aligned exactly 1 time 751522 (17.20%) aligned >1 times 91.53% overall alignment rate Time searching: 00:39:09 Overall time: 00:39:09 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] 2862587 / 16632623 = 0.1721 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 08:29:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7224573/SRX7224573.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7224573/SRX7224573.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7224573/SRX7224573.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7224573/SRX7224573.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 08:29:58: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:29:58: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:30:07: 1000000 INFO @ Tue, 14 Jul 2020 08:30:17: 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 08:30:27: 3000000 INFO @ Tue, 14 Jul 2020 08:30:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7224573/SRX7224573.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7224573/SRX7224573.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7224573/SRX7224573.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7224573/SRX7224573.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 08:30:28: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:30:28: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:30:37: 4000000 INFO @ Tue, 14 Jul 2020 08:30:37: 1000000 INFO @ Tue, 14 Jul 2020 08:30:46: 2000000 INFO @ Tue, 14 Jul 2020 08:30:47: 5000000 INFO @ Tue, 14 Jul 2020 08:30:55: 3000000 INFO @ Tue, 14 Jul 2020 08:30:56: 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 @ Tue, 14 Jul 2020 08:30:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7224573/SRX7224573.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7224573/SRX7224573.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7224573/SRX7224573.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7224573/SRX7224573.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 08:30:58: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:30:58: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:31:04: 4000000 INFO @ Tue, 14 Jul 2020 08:31:06: 7000000 INFO @ Tue, 14 Jul 2020 08:31:08: 1000000 INFO @ Tue, 14 Jul 2020 08:31:13: 5000000 INFO @ Tue, 14 Jul 2020 08:31:15: 8000000 INFO @ Tue, 14 Jul 2020 08:31:18: 2000000 INFO @ Tue, 14 Jul 2020 08:31:22: 6000000 INFO @ Tue, 14 Jul 2020 08:31:25: 9000000 INFO @ Tue, 14 Jul 2020 08:31:28: 3000000 INFO @ Tue, 14 Jul 2020 08:31:31: 7000000 INFO @ Tue, 14 Jul 2020 08:31:35: 10000000 INFO @ Tue, 14 Jul 2020 08:31:38: 4000000 INFO @ Tue, 14 Jul 2020 08:31:40: 8000000 INFO @ Tue, 14 Jul 2020 08:31:44: 11000000 INFO @ Tue, 14 Jul 2020 08:31:47: 5000000 INFO @ Tue, 14 Jul 2020 08:31:49: 9000000 INFO @ Tue, 14 Jul 2020 08:31:54: 12000000 INFO @ Tue, 14 Jul 2020 08:31:57: 6000000 INFO @ Tue, 14 Jul 2020 08:31:58: 10000000 INFO @ Tue, 14 Jul 2020 08:32:03: 13000000 INFO @ Tue, 14 Jul 2020 08:32:07: 11000000 INFO @ Tue, 14 Jul 2020 08:32:07: 7000000 INFO @ Tue, 14 Jul 2020 08:32:13: 14000000 INFO @ Tue, 14 Jul 2020 08:32:16: 12000000 INFO @ Tue, 14 Jul 2020 08:32:16: 8000000 INFO @ Tue, 14 Jul 2020 08:32:22: 15000000 INFO @ Tue, 14 Jul 2020 08:32:25: 13000000 INFO @ Tue, 14 Jul 2020 08:32:26: 9000000 INFO @ Tue, 14 Jul 2020 08:32:32: 16000000 INFO @ Tue, 14 Jul 2020 08:32:34: 14000000 INFO @ Tue, 14 Jul 2020 08:32:36: 10000000 INFO @ Tue, 14 Jul 2020 08:32:42: 17000000 INFO @ Tue, 14 Jul 2020 08:32:43: 15000000 INFO @ Tue, 14 Jul 2020 08:32:46: 11000000 INFO @ Tue, 14 Jul 2020 08:32:51: 18000000 INFO @ Tue, 14 Jul 2020 08:32:52: 16000000 INFO @ Tue, 14 Jul 2020 08:32:55: 12000000 INFO @ Tue, 14 Jul 2020 08:33:01: 17000000 INFO @ Tue, 14 Jul 2020 08:33:01: 19000000 INFO @ Tue, 14 Jul 2020 08:33:04: 13000000 INFO @ Tue, 14 Jul 2020 08:33:09: 18000000 INFO @ Tue, 14 Jul 2020 08:33:11: 20000000 INFO @ Tue, 14 Jul 2020 08:33:14: 14000000 INFO @ Tue, 14 Jul 2020 08:33:18: 19000000 INFO @ Tue, 14 Jul 2020 08:33:21: 21000000 INFO @ Tue, 14 Jul 2020 08:33:24: 15000000 INFO @ Tue, 14 Jul 2020 08:33:27: 20000000 INFO @ Tue, 14 Jul 2020 08:33:30: 22000000 INFO @ Tue, 14 Jul 2020 08:33:34: 16000000 INFO @ Tue, 14 Jul 2020 08:33:36: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 08:33:40: 23000000 INFO @ Tue, 14 Jul 2020 08:33:43: 17000000 INFO @ Tue, 14 Jul 2020 08:33:45: 22000000 INFO @ Tue, 14 Jul 2020 08:33:49: 24000000 INFO @ Tue, 14 Jul 2020 08:33:53: 18000000 INFO @ Tue, 14 Jul 2020 08:33:54: 23000000 INFO @ Tue, 14 Jul 2020 08:33:59: 25000000 INFO @ Tue, 14 Jul 2020 08:34:03: 19000000 INFO @ Tue, 14 Jul 2020 08:34:03: 24000000 INFO @ Tue, 14 Jul 2020 08:34:08: 26000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 08:34:11: 25000000 INFO @ Tue, 14 Jul 2020 08:34:12: 20000000 INFO @ Tue, 14 Jul 2020 08:34:17: 27000000 INFO @ Tue, 14 Jul 2020 08:34:20: 26000000 INFO @ Tue, 14 Jul 2020 08:34:22: 21000000 INFO @ Tue, 14 Jul 2020 08:34:27: 28000000 INFO @ Tue, 14 Jul 2020 08:34:28: 27000000 INFO @ Tue, 14 Jul 2020 08:34:32: 22000000 INFO @ Tue, 14 Jul 2020 08:34:36: 29000000 INFO @ Tue, 14 Jul 2020 08:34:37: 28000000 INFO @ Tue, 14 Jul 2020 08:34:38: #1 tag size is determined as 150 bps INFO @ Tue, 14 Jul 2020 08:34:38: #1 tag size = 150 INFO @ Tue, 14 Jul 2020 08:34:38: #1 total tags in treatment: 10991243 INFO @ Tue, 14 Jul 2020 08:34:38: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:34:38: #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 08:34:38: #1 tags after filtering in treatment: 8848058 INFO @ Tue, 14 Jul 2020 08:34:38: #1 Redundant rate of treatment: 0.19 INFO @ Tue, 14 Jul 2020 08:34:38: #1 finished! INFO @ Tue, 14 Jul 2020 08:34:38: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:34:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:34:40: #2 number of paired peaks: 13903 INFO @ Tue, 14 Jul 2020 08:34:40: start model_add_line... INFO @ Tue, 14 Jul 2020 08:34:40: start X-correlation... INFO @ Tue, 14 Jul 2020 08:34:40: end of X-cor INFO @ Tue, 14 Jul 2020 08:34:40: #2 finished! INFO @ Tue, 14 Jul 2020 08:34:40: #2 predicted fragment length is 165 bps INFO @ Tue, 14 Jul 2020 08:34:40: #2 alternative fragment length(s) may be 165 bps INFO @ Tue, 14 Jul 2020 08:34:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7224573/SRX7224573.05_model.r WARNING @ Tue, 14 Jul 2020 08:34:40: #2 Since the d (165) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:34:40: #2 You may need to consider one of the other alternative d(s): 165 WARNING @ Tue, 14 Jul 2020 08:34:40: #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 08:34:40: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:34:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:34:42: 23000000 INFO @ Tue, 14 Jul 2020 08:34:45: 29000000 INFO @ Tue, 14 Jul 2020 08:34:47: #1 tag size is determined as 150 bps INFO @ Tue, 14 Jul 2020 08:34:47: #1 tag size = 150 INFO @ Tue, 14 Jul 2020 08:34:47: #1 total tags in treatment: 10991243 INFO @ Tue, 14 Jul 2020 08:34:47: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:34:47: #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 08:34:47: #1 tags after filtering in treatment: 8848058 INFO @ Tue, 14 Jul 2020 08:34:47: #1 Redundant rate of treatment: 0.19 INFO @ Tue, 14 Jul 2020 08:34:47: #1 finished! INFO @ Tue, 14 Jul 2020 08:34:47: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:34:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:34:48: #2 number of paired peaks: 13903 INFO @ Tue, 14 Jul 2020 08:34:48: start model_add_line... INFO @ Tue, 14 Jul 2020 08:34:49: start X-correlation... INFO @ Tue, 14 Jul 2020 08:34:49: end of X-cor INFO @ Tue, 14 Jul 2020 08:34:49: #2 finished! INFO @ Tue, 14 Jul 2020 08:34:49: #2 predicted fragment length is 165 bps INFO @ Tue, 14 Jul 2020 08:34:49: #2 alternative fragment length(s) may be 165 bps INFO @ Tue, 14 Jul 2020 08:34:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7224573/SRX7224573.10_model.r WARNING @ Tue, 14 Jul 2020 08:34:49: #2 Since the d (165) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:34:49: #2 You may need to consider one of the other alternative d(s): 165 WARNING @ Tue, 14 Jul 2020 08:34:49: #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 08:34:49: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:34:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:34:51: 24000000 INFO @ Tue, 14 Jul 2020 08:35:00: 25000000 INFO @ Tue, 14 Jul 2020 08:35:03: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:35:09: 26000000 INFO @ Tue, 14 Jul 2020 08:35:14: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:35:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7224573/SRX7224573.05_peaks.xls INFO @ Tue, 14 Jul 2020 08:35:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7224573/SRX7224573.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:35:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7224573/SRX7224573.05_summits.bed INFO @ Tue, 14 Jul 2020 08:35:14: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8930 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:35:18: 27000000 INFO @ Tue, 14 Jul 2020 08:35:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7224573/SRX7224573.10_peaks.xls INFO @ Tue, 14 Jul 2020 08:35:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7224573/SRX7224573.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:35:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7224573/SRX7224573.10_summits.bed INFO @ Tue, 14 Jul 2020 08:35:26: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8208 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:35:27: 28000000 INFO @ Tue, 14 Jul 2020 08:35:35: 29000000 INFO @ Tue, 14 Jul 2020 08:35:37: #1 tag size is determined as 150 bps INFO @ Tue, 14 Jul 2020 08:35:37: #1 tag size = 150 INFO @ Tue, 14 Jul 2020 08:35:37: #1 total tags in treatment: 10991243 INFO @ Tue, 14 Jul 2020 08:35:37: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:35:37: #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 08:35:37: #1 tags after filtering in treatment: 8848058 INFO @ Tue, 14 Jul 2020 08:35:37: #1 Redundant rate of treatment: 0.19 INFO @ Tue, 14 Jul 2020 08:35:37: #1 finished! INFO @ Tue, 14 Jul 2020 08:35:37: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:35:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:35:38: #2 number of paired peaks: 13903 INFO @ Tue, 14 Jul 2020 08:35:38: start model_add_line... INFO @ Tue, 14 Jul 2020 08:35:39: start X-correlation... INFO @ Tue, 14 Jul 2020 08:35:39: end of X-cor INFO @ Tue, 14 Jul 2020 08:35:39: #2 finished! INFO @ Tue, 14 Jul 2020 08:35:39: #2 predicted fragment length is 165 bps INFO @ Tue, 14 Jul 2020 08:35:39: #2 alternative fragment length(s) may be 165 bps INFO @ Tue, 14 Jul 2020 08:35:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7224573/SRX7224573.20_model.r WARNING @ Tue, 14 Jul 2020 08:35:39: #2 Since the d (165) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:35:39: #2 You may need to consider one of the other alternative d(s): 165 WARNING @ Tue, 14 Jul 2020 08:35:39: #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 08:35:39: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:35:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:36:01: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:36:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7224573/SRX7224573.20_peaks.xls INFO @ Tue, 14 Jul 2020 08:36:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7224573/SRX7224573.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:36:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7224573/SRX7224573.20_summits.bed INFO @ Tue, 14 Jul 2020 08:36:12: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (7175 records, 4 fields): 21 millis CompletedMACS2peakCalling