Job ID = 6626566 SRX = SRX7224548 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 19542184 spots for SRR10541156/SRR10541156.sra Written 19542184 spots for SRR10541156/SRR10541156.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626738 ("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: 00:23:47 19542184 reads; of these: 19542184 (100.00%) were paired; of these: 1153933 (5.90%) aligned concordantly 0 times 17490098 (89.50%) aligned concordantly exactly 1 time 898153 (4.60%) aligned concordantly >1 times ---- 1153933 pairs aligned concordantly 0 times; of these: 103327 (8.95%) aligned discordantly 1 time ---- 1050606 pairs aligned 0 times concordantly or discordantly; of these: 2101212 mates make up the pairs; of these: 1451280 (69.07%) aligned 0 times 484821 (23.07%) aligned exactly 1 time 165111 (7.86%) aligned >1 times 96.29% overall alignment rate Time searching: 00:23:47 Overall time: 00:23:47 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] 1125527 / 18417276 = 0.0611 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 08:08:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7224548/SRX7224548.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7224548/SRX7224548.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7224548/SRX7224548.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7224548/SRX7224548.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 08:08:16: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:08:16: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:08:22: 1000000 INFO @ Tue, 14 Jul 2020 08:08:29: 2000000 INFO @ Tue, 14 Jul 2020 08:08:35: 3000000 INFO @ Tue, 14 Jul 2020 08:08:41: 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 @ Tue, 14 Jul 2020 08:08:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7224548/SRX7224548.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7224548/SRX7224548.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7224548/SRX7224548.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7224548/SRX7224548.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 08:08:46: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:08:46: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:08:48: 5000000 INFO @ Tue, 14 Jul 2020 08:08:53: 1000000 INFO @ Tue, 14 Jul 2020 08:08:56: 6000000 INFO @ Tue, 14 Jul 2020 08:09:01: 2000000 INFO @ Tue, 14 Jul 2020 08:09:03: 7000000 INFO @ Tue, 14 Jul 2020 08:09:08: 3000000 INFO @ Tue, 14 Jul 2020 08:09:10: 8000000 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 08:09:15: 4000000 INFO @ Tue, 14 Jul 2020 08:09:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7224548/SRX7224548.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7224548/SRX7224548.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7224548/SRX7224548.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7224548/SRX7224548.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 08:09:16: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:09:16: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:09:18: 9000000 INFO @ Tue, 14 Jul 2020 08:09:23: 5000000 INFO @ Tue, 14 Jul 2020 08:09:23: 1000000 INFO @ Tue, 14 Jul 2020 08:09:25: 10000000 INFO @ Tue, 14 Jul 2020 08:09:30: 6000000 INFO @ Tue, 14 Jul 2020 08:09:31: 2000000 INFO @ Tue, 14 Jul 2020 08:09:32: 11000000 INFO @ Tue, 14 Jul 2020 08:09:38: 7000000 INFO @ Tue, 14 Jul 2020 08:09:38: 3000000 INFO @ Tue, 14 Jul 2020 08:09:40: 12000000 INFO @ Tue, 14 Jul 2020 08:09:46: 8000000 INFO @ Tue, 14 Jul 2020 08:09:46: 4000000 INFO @ Tue, 14 Jul 2020 08:09:47: 13000000 INFO @ Tue, 14 Jul 2020 08:09:53: 9000000 INFO @ Tue, 14 Jul 2020 08:09:53: 5000000 INFO @ Tue, 14 Jul 2020 08:09:55: 14000000 INFO @ Tue, 14 Jul 2020 08:10:01: 10000000 INFO @ Tue, 14 Jul 2020 08:10:01: 6000000 INFO @ Tue, 14 Jul 2020 08:10:02: 15000000 INFO @ Tue, 14 Jul 2020 08:10:08: 11000000 INFO @ Tue, 14 Jul 2020 08:10:08: 7000000 INFO @ Tue, 14 Jul 2020 08:10:09: 16000000 INFO @ Tue, 14 Jul 2020 08:10:15: 8000000 INFO @ Tue, 14 Jul 2020 08:10:15: 12000000 INFO @ Tue, 14 Jul 2020 08:10:17: 17000000 INFO @ Tue, 14 Jul 2020 08:10:23: 9000000 INFO @ Tue, 14 Jul 2020 08:10:23: 13000000 INFO @ Tue, 14 Jul 2020 08:10:24: 18000000 INFO @ Tue, 14 Jul 2020 08:10:30: 10000000 INFO @ Tue, 14 Jul 2020 08:10:30: 14000000 INFO @ Tue, 14 Jul 2020 08:10:32: 19000000 INFO @ Tue, 14 Jul 2020 08:10:38: 11000000 INFO @ Tue, 14 Jul 2020 08:10:38: 15000000 INFO @ Tue, 14 Jul 2020 08:10:39: 20000000 INFO @ Tue, 14 Jul 2020 08:10:45: 12000000 INFO @ Tue, 14 Jul 2020 08:10:45: 16000000 INFO @ Tue, 14 Jul 2020 08:10:46: 21000000 INFO @ Tue, 14 Jul 2020 08:10:52: 13000000 INFO @ Tue, 14 Jul 2020 08:10:53: 17000000 INFO @ Tue, 14 Jul 2020 08:10:53: 22000000 INFO @ Tue, 14 Jul 2020 08:11:00: 14000000 INFO @ Tue, 14 Jul 2020 08:11:00: 18000000 INFO @ Tue, 14 Jul 2020 08:11:01: 23000000 INFO @ Tue, 14 Jul 2020 08:11:07: 15000000 INFO @ Tue, 14 Jul 2020 08:11:07: 19000000 INFO @ Tue, 14 Jul 2020 08:11:08: 24000000 INFO @ Tue, 14 Jul 2020 08:11:15: 16000000 INFO @ Tue, 14 Jul 2020 08:11:15: 20000000 INFO @ Tue, 14 Jul 2020 08:11:16: 25000000 INFO @ Tue, 14 Jul 2020 08:11:22: 17000000 INFO @ Tue, 14 Jul 2020 08:11:22: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 08:11:23: 26000000 INFO @ Tue, 14 Jul 2020 08:11:29: 18000000 INFO @ Tue, 14 Jul 2020 08:11:30: 22000000 INFO @ Tue, 14 Jul 2020 08:11:30: 27000000 INFO @ Tue, 14 Jul 2020 08:11:37: 19000000 INFO @ Tue, 14 Jul 2020 08:11:37: 23000000 INFO @ Tue, 14 Jul 2020 08:11:38: 28000000 INFO @ Tue, 14 Jul 2020 08:11:44: 20000000 INFO @ Tue, 14 Jul 2020 08:11:44: 24000000 INFO @ Tue, 14 Jul 2020 08:11:45: 29000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 08:11:51: 21000000 INFO @ Tue, 14 Jul 2020 08:11:52: 25000000 INFO @ Tue, 14 Jul 2020 08:11:52: 30000000 INFO @ Tue, 14 Jul 2020 08:11:59: 22000000 INFO @ Tue, 14 Jul 2020 08:11:59: 26000000 INFO @ Tue, 14 Jul 2020 08:12:00: 31000000 INFO @ Tue, 14 Jul 2020 08:12:06: 23000000 INFO @ Tue, 14 Jul 2020 08:12:07: 27000000 INFO @ Tue, 14 Jul 2020 08:12:07: 32000000 INFO @ Tue, 14 Jul 2020 08:12:13: 24000000 INFO @ Tue, 14 Jul 2020 08:12:14: 28000000 INFO @ Tue, 14 Jul 2020 08:12:15: 33000000 INFO @ Tue, 14 Jul 2020 08:12:21: 25000000 INFO @ Tue, 14 Jul 2020 08:12:22: 29000000 INFO @ Tue, 14 Jul 2020 08:12:22: 34000000 INFO @ Tue, 14 Jul 2020 08:12:28: 26000000 INFO @ Tue, 14 Jul 2020 08:12:29: 30000000 INFO @ Tue, 14 Jul 2020 08:12:30: 35000000 INFO @ Tue, 14 Jul 2020 08:12:33: #1 tag size is determined as 78 bps INFO @ Tue, 14 Jul 2020 08:12:33: #1 tag size = 78 INFO @ Tue, 14 Jul 2020 08:12:33: #1 total tags in treatment: 17264136 INFO @ Tue, 14 Jul 2020 08:12:33: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:12:33: #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 08:12:33: #1 tags after filtering in treatment: 12449824 INFO @ Tue, 14 Jul 2020 08:12:33: #1 Redundant rate of treatment: 0.28 INFO @ Tue, 14 Jul 2020 08:12:33: #1 finished! INFO @ Tue, 14 Jul 2020 08:12:33: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:12:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:12:35: #2 number of paired peaks: 14545 INFO @ Tue, 14 Jul 2020 08:12:35: start model_add_line... INFO @ Tue, 14 Jul 2020 08:12:35: start X-correlation... INFO @ Tue, 14 Jul 2020 08:12:35: end of X-cor INFO @ Tue, 14 Jul 2020 08:12:35: #2 finished! INFO @ Tue, 14 Jul 2020 08:12:35: #2 predicted fragment length is 148 bps INFO @ Tue, 14 Jul 2020 08:12:35: #2 alternative fragment length(s) may be 148 bps INFO @ Tue, 14 Jul 2020 08:12:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7224548/SRX7224548.05_model.r WARNING @ Tue, 14 Jul 2020 08:12:35: #2 Since the d (148) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:12:35: #2 You may need to consider one of the other alternative d(s): 148 WARNING @ Tue, 14 Jul 2020 08:12:35: #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 08:12:35: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:12:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:12:35: 27000000 INFO @ Tue, 14 Jul 2020 08:12:36: 31000000 INFO @ Tue, 14 Jul 2020 08:12:43: 28000000 INFO @ Tue, 14 Jul 2020 08:12:44: 32000000 INFO @ Tue, 14 Jul 2020 08:12:50: 29000000 INFO @ Tue, 14 Jul 2020 08:12:51: 33000000 INFO @ Tue, 14 Jul 2020 08:12:58: 30000000 INFO @ Tue, 14 Jul 2020 08:12:59: 34000000 INFO @ Tue, 14 Jul 2020 08:13:05: 31000000 INFO @ Tue, 14 Jul 2020 08:13:06: 35000000 INFO @ Tue, 14 Jul 2020 08:13:07: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:13:09: #1 tag size is determined as 78 bps INFO @ Tue, 14 Jul 2020 08:13:09: #1 tag size = 78 INFO @ Tue, 14 Jul 2020 08:13:09: #1 total tags in treatment: 17264136 INFO @ Tue, 14 Jul 2020 08:13:09: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:13:09: #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 08:13:09: #1 tags after filtering in treatment: 12449824 INFO @ Tue, 14 Jul 2020 08:13:09: #1 Redundant rate of treatment: 0.28 INFO @ Tue, 14 Jul 2020 08:13:09: #1 finished! INFO @ Tue, 14 Jul 2020 08:13:09: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:13:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:13:11: #2 number of paired peaks: 14545 INFO @ Tue, 14 Jul 2020 08:13:11: start model_add_line... INFO @ Tue, 14 Jul 2020 08:13:11: start X-correlation... INFO @ Tue, 14 Jul 2020 08:13:11: end of X-cor INFO @ Tue, 14 Jul 2020 08:13:11: #2 finished! INFO @ Tue, 14 Jul 2020 08:13:11: #2 predicted fragment length is 148 bps INFO @ Tue, 14 Jul 2020 08:13:11: #2 alternative fragment length(s) may be 148 bps INFO @ Tue, 14 Jul 2020 08:13:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7224548/SRX7224548.10_model.r WARNING @ Tue, 14 Jul 2020 08:13:11: #2 Since the d (148) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:13:11: #2 You may need to consider one of the other alternative d(s): 148 WARNING @ Tue, 14 Jul 2020 08:13:11: #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 08:13:11: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:13:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:13:12: 32000000 INFO @ Tue, 14 Jul 2020 08:13:18: 33000000 INFO @ Tue, 14 Jul 2020 08:13:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7224548/SRX7224548.05_peaks.xls INFO @ Tue, 14 Jul 2020 08:13:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7224548/SRX7224548.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:13:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7224548/SRX7224548.05_summits.bed INFO @ Tue, 14 Jul 2020 08:13:21: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9029 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:13:25: 34000000 INFO @ Tue, 14 Jul 2020 08:13:31: 35000000 INFO @ Tue, 14 Jul 2020 08:13:33: #1 tag size is determined as 78 bps INFO @ Tue, 14 Jul 2020 08:13:33: #1 tag size = 78 INFO @ Tue, 14 Jul 2020 08:13:33: #1 total tags in treatment: 17264136 INFO @ Tue, 14 Jul 2020 08:13:33: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:13:33: #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 08:13:34: #1 tags after filtering in treatment: 12449824 INFO @ Tue, 14 Jul 2020 08:13:34: #1 Redundant rate of treatment: 0.28 INFO @ Tue, 14 Jul 2020 08:13:34: #1 finished! INFO @ Tue, 14 Jul 2020 08:13:34: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:13:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:13:35: #2 number of paired peaks: 14545 INFO @ Tue, 14 Jul 2020 08:13:35: start model_add_line... INFO @ Tue, 14 Jul 2020 08:13:36: start X-correlation... INFO @ Tue, 14 Jul 2020 08:13:36: end of X-cor INFO @ Tue, 14 Jul 2020 08:13:36: #2 finished! INFO @ Tue, 14 Jul 2020 08:13:36: #2 predicted fragment length is 148 bps INFO @ Tue, 14 Jul 2020 08:13:36: #2 alternative fragment length(s) may be 148 bps INFO @ Tue, 14 Jul 2020 08:13:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7224548/SRX7224548.20_model.r WARNING @ Tue, 14 Jul 2020 08:13:36: #2 Since the d (148) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:13:36: #2 You may need to consider one of the other alternative d(s): 148 WARNING @ Tue, 14 Jul 2020 08:13:36: #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 08:13:36: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:13:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:13:41: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:13:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7224548/SRX7224548.10_peaks.xls INFO @ Tue, 14 Jul 2020 08:13:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7224548/SRX7224548.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:13:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7224548/SRX7224548.10_summits.bed INFO @ Tue, 14 Jul 2020 08:13:54: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (8365 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:14:06: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:14:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7224548/SRX7224548.20_peaks.xls INFO @ Tue, 14 Jul 2020 08:14:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7224548/SRX7224548.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:14:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7224548/SRX7224548.20_summits.bed INFO @ Tue, 14 Jul 2020 08:14:20: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (7445 records, 4 fields): 22 millis CompletedMACS2peakCalling