Job ID = 6626520 SRX = SRX5736494 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 11963086 spots for SRR8956905/SRR8956905.sra Written 11963086 spots for SRR8956905/SRR8956905.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626725 ("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: 00:33:29 11963086 reads; of these: 11963086 (100.00%) were paired; of these: 1923861 (16.08%) aligned concordantly 0 times 6542751 (54.69%) aligned concordantly exactly 1 time 3496474 (29.23%) aligned concordantly >1 times ---- 1923861 pairs aligned concordantly 0 times; of these: 499757 (25.98%) aligned discordantly 1 time ---- 1424104 pairs aligned 0 times concordantly or discordantly; of these: 2848208 mates make up the pairs; of these: 1681956 (59.05%) aligned 0 times 505031 (17.73%) aligned exactly 1 time 661221 (23.22%) aligned >1 times 92.97% overall alignment rate Time searching: 00:33:29 Overall time: 00:33:29 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] 545584 / 10513217 = 0.0519 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 07:59:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736494/SRX5736494.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736494/SRX5736494.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736494/SRX5736494.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736494/SRX5736494.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 07:59:08: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:59:08: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:59:15: 1000000 INFO @ Tue, 14 Jul 2020 07:59:22: 2000000 INFO @ Tue, 14 Jul 2020 07:59:29: 3000000 INFO @ Tue, 14 Jul 2020 07:59:36: 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 07:59:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736494/SRX5736494.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736494/SRX5736494.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736494/SRX5736494.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736494/SRX5736494.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 07:59:38: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:59:38: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:59:43: 5000000 INFO @ Tue, 14 Jul 2020 07:59:46: 1000000 INFO @ Tue, 14 Jul 2020 07:59:51: 6000000 INFO @ Tue, 14 Jul 2020 07:59:56: 2000000 INFO @ Tue, 14 Jul 2020 07:59:59: 7000000 INFO @ Tue, 14 Jul 2020 08:00:06: 3000000 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 08:00:07: 8000000 INFO @ Tue, 14 Jul 2020 08:00:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736494/SRX5736494.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736494/SRX5736494.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736494/SRX5736494.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736494/SRX5736494.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 08:00:10: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:00:10: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:00:14: 4000000 INFO @ Tue, 14 Jul 2020 08:00:15: 9000000 INFO @ Tue, 14 Jul 2020 08:00:19: 1000000 INFO @ Tue, 14 Jul 2020 08:00:22: 5000000 INFO @ Tue, 14 Jul 2020 08:00:22: 10000000 INFO @ Tue, 14 Jul 2020 08:00:27: 2000000 INFO @ Tue, 14 Jul 2020 08:00:30: 6000000 INFO @ Tue, 14 Jul 2020 08:00:30: 11000000 INFO @ Tue, 14 Jul 2020 08:00:36: 3000000 INFO @ Tue, 14 Jul 2020 08:00:38: 12000000 INFO @ Tue, 14 Jul 2020 08:00:39: 7000000 INFO @ Tue, 14 Jul 2020 08:00:44: 4000000 INFO @ Tue, 14 Jul 2020 08:00:46: 13000000 INFO @ Tue, 14 Jul 2020 08:00:47: 8000000 INFO @ Tue, 14 Jul 2020 08:00:52: 5000000 INFO @ Tue, 14 Jul 2020 08:00:54: 14000000 INFO @ Tue, 14 Jul 2020 08:00:54: 9000000 INFO @ Tue, 14 Jul 2020 08:01:00: 6000000 INFO @ Tue, 14 Jul 2020 08:01:02: 15000000 INFO @ Tue, 14 Jul 2020 08:01:02: 10000000 INFO @ Tue, 14 Jul 2020 08:01:09: 7000000 INFO @ Tue, 14 Jul 2020 08:01:10: 16000000 INFO @ Tue, 14 Jul 2020 08:01:10: 11000000 INFO @ Tue, 14 Jul 2020 08:01:17: 8000000 INFO @ Tue, 14 Jul 2020 08:01:18: 17000000 INFO @ Tue, 14 Jul 2020 08:01:18: 12000000 INFO @ Tue, 14 Jul 2020 08:01:26: 9000000 INFO @ Tue, 14 Jul 2020 08:01:26: 13000000 INFO @ Tue, 14 Jul 2020 08:01:27: 18000000 INFO @ Tue, 14 Jul 2020 08:01:34: 10000000 INFO @ Tue, 14 Jul 2020 08:01:34: 14000000 INFO @ Tue, 14 Jul 2020 08:01:35: 19000000 INFO @ Tue, 14 Jul 2020 08:01:43: 15000000 INFO @ Tue, 14 Jul 2020 08:01:43: 11000000 INFO @ Tue, 14 Jul 2020 08:01:43: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 08:01:51: 16000000 INFO @ Tue, 14 Jul 2020 08:01:51: 12000000 INFO @ Tue, 14 Jul 2020 08:01:51: 21000000 INFO @ Tue, 14 Jul 2020 08:01:53: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:01:53: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:01:53: #1 total tags in treatment: 9506761 INFO @ Tue, 14 Jul 2020 08:01:53: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:01:53: #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 08:01:53: #1 tags after filtering in treatment: 8630381 INFO @ Tue, 14 Jul 2020 08:01:53: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 14 Jul 2020 08:01:53: #1 finished! INFO @ Tue, 14 Jul 2020 08:01:53: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:01:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:01:53: #2 number of paired peaks: 227 WARNING @ Tue, 14 Jul 2020 08:01:53: Fewer paired peaks (227) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 227 pairs to build model! INFO @ Tue, 14 Jul 2020 08:01:53: start model_add_line... INFO @ Tue, 14 Jul 2020 08:01:53: start X-correlation... INFO @ Tue, 14 Jul 2020 08:01:53: end of X-cor INFO @ Tue, 14 Jul 2020 08:01:53: #2 finished! INFO @ Tue, 14 Jul 2020 08:01:53: #2 predicted fragment length is 141 bps INFO @ Tue, 14 Jul 2020 08:01:53: #2 alternative fragment length(s) may be 141 bps INFO @ Tue, 14 Jul 2020 08:01:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736494/SRX5736494.05_model.r WARNING @ Tue, 14 Jul 2020 08:01:53: #2 Since the d (141) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:01:53: #2 You may need to consider one of the other alternative d(s): 141 WARNING @ Tue, 14 Jul 2020 08:01:53: #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 08:01:53: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:01:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:01:59: 17000000 INFO @ Tue, 14 Jul 2020 08:01:59: 13000000 INFO @ Tue, 14 Jul 2020 08:02:08: 14000000 INFO @ Tue, 14 Jul 2020 08:02:08: 18000000 INFO @ Tue, 14 Jul 2020 08:02:11: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:02:16: 15000000 INFO @ Tue, 14 Jul 2020 08:02:16: 19000000 INFO @ Tue, 14 Jul 2020 08:02:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736494/SRX5736494.05_peaks.xls INFO @ Tue, 14 Jul 2020 08:02:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736494/SRX5736494.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:02:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736494/SRX5736494.05_summits.bed INFO @ Tue, 14 Jul 2020 08:02:20: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (2290 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:02:24: 20000000 INFO @ Tue, 14 Jul 2020 08:02:24: 16000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 08:02:32: 21000000 INFO @ Tue, 14 Jul 2020 08:02:32: 17000000 INFO @ Tue, 14 Jul 2020 08:02:33: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:02:33: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:02:33: #1 total tags in treatment: 9506761 INFO @ Tue, 14 Jul 2020 08:02:33: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:02:33: #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 08:02:33: #1 tags after filtering in treatment: 8630381 INFO @ Tue, 14 Jul 2020 08:02:33: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 14 Jul 2020 08:02:33: #1 finished! INFO @ Tue, 14 Jul 2020 08:02:33: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:02:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:02:33: #2 number of paired peaks: 227 WARNING @ Tue, 14 Jul 2020 08:02:33: Fewer paired peaks (227) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 227 pairs to build model! INFO @ Tue, 14 Jul 2020 08:02:33: start model_add_line... INFO @ Tue, 14 Jul 2020 08:02:34: start X-correlation... INFO @ Tue, 14 Jul 2020 08:02:34: end of X-cor INFO @ Tue, 14 Jul 2020 08:02:34: #2 finished! INFO @ Tue, 14 Jul 2020 08:02:34: #2 predicted fragment length is 141 bps INFO @ Tue, 14 Jul 2020 08:02:34: #2 alternative fragment length(s) may be 141 bps INFO @ Tue, 14 Jul 2020 08:02:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736494/SRX5736494.10_model.r WARNING @ Tue, 14 Jul 2020 08:02:34: #2 Since the d (141) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:02:34: #2 You may need to consider one of the other alternative d(s): 141 WARNING @ Tue, 14 Jul 2020 08:02:34: #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 08:02:34: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:02:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:02:39: 18000000 INFO @ Tue, 14 Jul 2020 08:02:46: 19000000 INFO @ Tue, 14 Jul 2020 08:02:51: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:02:54: 20000000 INFO @ Tue, 14 Jul 2020 08:02:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736494/SRX5736494.10_peaks.xls INFO @ Tue, 14 Jul 2020 08:02:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736494/SRX5736494.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:02:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736494/SRX5736494.10_summits.bed INFO @ Tue, 14 Jul 2020 08:02:59: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (853 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:03:02: 21000000 INFO @ Tue, 14 Jul 2020 08:03:03: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:03:03: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:03:03: #1 total tags in treatment: 9506761 INFO @ Tue, 14 Jul 2020 08:03:03: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:03:03: #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 08:03:03: #1 tags after filtering in treatment: 8630381 INFO @ Tue, 14 Jul 2020 08:03:03: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 14 Jul 2020 08:03:03: #1 finished! INFO @ Tue, 14 Jul 2020 08:03:03: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:03:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:03:03: #2 number of paired peaks: 227 WARNING @ Tue, 14 Jul 2020 08:03:03: Fewer paired peaks (227) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 227 pairs to build model! INFO @ Tue, 14 Jul 2020 08:03:03: start model_add_line... INFO @ Tue, 14 Jul 2020 08:03:03: start X-correlation... INFO @ Tue, 14 Jul 2020 08:03:03: end of X-cor INFO @ Tue, 14 Jul 2020 08:03:03: #2 finished! INFO @ Tue, 14 Jul 2020 08:03:03: #2 predicted fragment length is 141 bps INFO @ Tue, 14 Jul 2020 08:03:03: #2 alternative fragment length(s) may be 141 bps INFO @ Tue, 14 Jul 2020 08:03:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736494/SRX5736494.20_model.r WARNING @ Tue, 14 Jul 2020 08:03:03: #2 Since the d (141) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:03:03: #2 You may need to consider one of the other alternative d(s): 141 WARNING @ Tue, 14 Jul 2020 08:03:03: #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 08:03:03: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:03:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:03:21: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:03:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736494/SRX5736494.20_peaks.xls INFO @ Tue, 14 Jul 2020 08:03:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736494/SRX5736494.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:03:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736494/SRX5736494.20_summits.bed INFO @ Tue, 14 Jul 2020 08:03:30: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (450 records, 4 fields): 2 millis CompletedMACS2peakCalling