Job ID = 14171374 SRX = SRX9986165 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 21062679 spots for SRR13591519/SRR13591519.sra Written 21062679 spots for SRR13591519/SRR13591519.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171861 ("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: 00:06:10 21062679 reads; of these: 21062679 (100.00%) were unpaired; of these: 1978861 (9.40%) aligned 0 times 16230306 (77.06%) aligned exactly 1 time 2853512 (13.55%) aligned >1 times 90.60% overall alignment rate Time searching: 00:06:10 Overall time: 00:06:10 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_rmdupse_core] 5624503 / 19083818 = 0.2947 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 11:39:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986165/SRX9986165.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986165/SRX9986165.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986165/SRX9986165.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986165/SRX9986165.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 @ Sat, 11 Dec 2021 11:39:59: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:39:59: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:40:07: 1000000 INFO @ Sat, 11 Dec 2021 11:40:16: 2000000 INFO @ Sat, 11 Dec 2021 11:40:25: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 11:40:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986165/SRX9986165.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986165/SRX9986165.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986165/SRX9986165.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986165/SRX9986165.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 @ Sat, 11 Dec 2021 11:40:29: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:40:29: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:40:33: 4000000 INFO @ Sat, 11 Dec 2021 11:40:38: 1000000 INFO @ Sat, 11 Dec 2021 11:40:41: 5000000 INFO @ Sat, 11 Dec 2021 11:40:46: 2000000 INFO @ Sat, 11 Dec 2021 11:40:50: 6000000 INFO @ Sat, 11 Dec 2021 11:40:55: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 11:40:59: 7000000 INFO @ Sat, 11 Dec 2021 11:40:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986165/SRX9986165.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986165/SRX9986165.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986165/SRX9986165.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986165/SRX9986165.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 @ Sat, 11 Dec 2021 11:40:59: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:40:59: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:41:03: 4000000 INFO @ Sat, 11 Dec 2021 11:41:07: 8000000 INFO @ Sat, 11 Dec 2021 11:41:08: 1000000 INFO @ Sat, 11 Dec 2021 11:41:12: 5000000 INFO @ Sat, 11 Dec 2021 11:41:17: 9000000 INFO @ Sat, 11 Dec 2021 11:41:19: 2000000 INFO @ Sat, 11 Dec 2021 11:41:21: 6000000 INFO @ Sat, 11 Dec 2021 11:41:26: 10000000 INFO @ Sat, 11 Dec 2021 11:41:29: 3000000 INFO @ Sat, 11 Dec 2021 11:41:30: 7000000 INFO @ Sat, 11 Dec 2021 11:41:35: 11000000 INFO @ Sat, 11 Dec 2021 11:41:38: 4000000 INFO @ Sat, 11 Dec 2021 11:41:38: 8000000 INFO @ Sat, 11 Dec 2021 11:41:45: 12000000 INFO @ Sat, 11 Dec 2021 11:41:49: 5000000 INFO @ Sat, 11 Dec 2021 11:41:49: 9000000 INFO @ Sat, 11 Dec 2021 11:41:57: 13000000 INFO @ Sat, 11 Dec 2021 11:41:58: 10000000 INFO @ Sat, 11 Dec 2021 11:41:58: 6000000 INFO @ Sat, 11 Dec 2021 11:42:01: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 11:42:01: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 11:42:01: #1 total tags in treatment: 13459315 INFO @ Sat, 11 Dec 2021 11:42:01: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:42:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 11:42:01: #1 tags after filtering in treatment: 13459315 INFO @ Sat, 11 Dec 2021 11:42:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:42:01: #1 finished! INFO @ Sat, 11 Dec 2021 11:42:01: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:42:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:42:03: #2 number of paired peaks: 141 WARNING @ Sat, 11 Dec 2021 11:42:03: Fewer paired peaks (141) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 141 pairs to build model! INFO @ Sat, 11 Dec 2021 11:42:03: start model_add_line... INFO @ Sat, 11 Dec 2021 11:42:03: start X-correlation... INFO @ Sat, 11 Dec 2021 11:42:03: end of X-cor INFO @ Sat, 11 Dec 2021 11:42:03: #2 finished! INFO @ Sat, 11 Dec 2021 11:42:03: #2 predicted fragment length is 207 bps INFO @ Sat, 11 Dec 2021 11:42:03: #2 alternative fragment length(s) may be 0,153,179,207,264 bps INFO @ Sat, 11 Dec 2021 11:42:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986165/SRX9986165.05_model.r INFO @ Sat, 11 Dec 2021 11:42:03: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:42:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:42:06: 11000000 INFO @ Sat, 11 Dec 2021 11:42:06: 7000000 INFO @ Sat, 11 Dec 2021 11:42:16: 8000000 INFO @ Sat, 11 Dec 2021 11:42:16: 12000000 INFO @ Sat, 11 Dec 2021 11:42:25: 13000000 INFO @ Sat, 11 Dec 2021 11:42:25: 9000000 INFO @ Sat, 11 Dec 2021 11:42:30: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 11:42:30: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 11:42:30: #1 total tags in treatment: 13459315 INFO @ Sat, 11 Dec 2021 11:42:30: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:42:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 11:42:30: #1 tags after filtering in treatment: 13459315 INFO @ Sat, 11 Dec 2021 11:42:30: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:42:30: #1 finished! INFO @ Sat, 11 Dec 2021 11:42:30: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:42:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:42:32: #2 number of paired peaks: 141 WARNING @ Sat, 11 Dec 2021 11:42:32: Fewer paired peaks (141) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 141 pairs to build model! INFO @ Sat, 11 Dec 2021 11:42:32: start model_add_line... INFO @ Sat, 11 Dec 2021 11:42:32: start X-correlation... INFO @ Sat, 11 Dec 2021 11:42:32: end of X-cor INFO @ Sat, 11 Dec 2021 11:42:32: #2 finished! INFO @ Sat, 11 Dec 2021 11:42:32: #2 predicted fragment length is 207 bps INFO @ Sat, 11 Dec 2021 11:42:32: #2 alternative fragment length(s) may be 0,153,179,207,264 bps INFO @ Sat, 11 Dec 2021 11:42:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986165/SRX9986165.10_model.r INFO @ Sat, 11 Dec 2021 11:42:32: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:42:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:42:36: 10000000 INFO @ Sat, 11 Dec 2021 11:42:46: 11000000 INFO @ Sat, 11 Dec 2021 11:42:50: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:42:56: 12000000 INFO @ Sat, 11 Dec 2021 11:43:06: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:43:10: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 11:43:10: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 11:43:10: #1 total tags in treatment: 13459315 INFO @ Sat, 11 Dec 2021 11:43:10: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:43:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 11:43:10: #1 tags after filtering in treatment: 13459315 INFO @ Sat, 11 Dec 2021 11:43:10: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:43:10: #1 finished! INFO @ Sat, 11 Dec 2021 11:43:10: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:43:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:43:11: #2 number of paired peaks: 141 WARNING @ Sat, 11 Dec 2021 11:43:11: Fewer paired peaks (141) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 141 pairs to build model! INFO @ Sat, 11 Dec 2021 11:43:11: start model_add_line... INFO @ Sat, 11 Dec 2021 11:43:12: start X-correlation... INFO @ Sat, 11 Dec 2021 11:43:12: end of X-cor INFO @ Sat, 11 Dec 2021 11:43:12: #2 finished! INFO @ Sat, 11 Dec 2021 11:43:12: #2 predicted fragment length is 207 bps INFO @ Sat, 11 Dec 2021 11:43:12: #2 alternative fragment length(s) may be 0,153,179,207,264 bps INFO @ Sat, 11 Dec 2021 11:43:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986165/SRX9986165.20_model.r INFO @ Sat, 11 Dec 2021 11:43:12: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:43:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:43:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986165/SRX9986165.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:43:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986165/SRX9986165.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:43:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986165/SRX9986165.05_summits.bed INFO @ Sat, 11 Dec 2021 11:43:13: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (4782 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:43:19: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:43:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986165/SRX9986165.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:43:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986165/SRX9986165.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:43:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986165/SRX9986165.10_summits.bed INFO @ Sat, 11 Dec 2021 11:43:39: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1648 records, 4 fields): 7 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:43:53: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:44:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986165/SRX9986165.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:44:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986165/SRX9986165.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:44:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986165/SRX9986165.20_summits.bed INFO @ Sat, 11 Dec 2021 11:44:13: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (242 records, 4 fields): 2 millis CompletedMACS2peakCalling