Job ID = 14167046 SRX = SRX8574277 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 54185096 spots for SRR12045598/SRR12045598.sra Written 54185096 spots for SRR12045598/SRR12045598.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167479 ("srTdm6") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:22:35 54185096 reads; of these: 54185096 (100.00%) were unpaired; of these: 7993833 (14.75%) aligned 0 times 33393937 (61.63%) aligned exactly 1 time 12797326 (23.62%) aligned >1 times 85.25% overall alignment rate Time searching: 00:22:36 Overall time: 00:22:36 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 20 files... [bam_rmdupse_core] 11893929 / 46191263 = 0.2575 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 @ Fri, 10 Dec 2021 09:55:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8574277/SRX8574277.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8574277/SRX8574277.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8574277/SRX8574277.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8574277/SRX8574277.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, 10 Dec 2021 09:55:38: #1 read tag files... INFO @ Fri, 10 Dec 2021 09:55:38: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 09:55:45: 1000000 INFO @ Fri, 10 Dec 2021 09:55:53: 2000000 INFO @ Fri, 10 Dec 2021 09:56:00: 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 @ Fri, 10 Dec 2021 09:56:06: 4000000 INFO @ Fri, 10 Dec 2021 09:56:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8574277/SRX8574277.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8574277/SRX8574277.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8574277/SRX8574277.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8574277/SRX8574277.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, 10 Dec 2021 09:56:07: #1 read tag files... INFO @ Fri, 10 Dec 2021 09:56:07: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 09:56:14: 5000000 INFO @ Fri, 10 Dec 2021 09:56:15: 1000000 INFO @ Fri, 10 Dec 2021 09:56:21: 6000000 INFO @ Fri, 10 Dec 2021 09:56:22: 2000000 INFO @ Fri, 10 Dec 2021 09:56:30: 7000000 INFO @ Fri, 10 Dec 2021 09:56:30: 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 @ Fri, 10 Dec 2021 09:56:37: 4000000 INFO @ Fri, 10 Dec 2021 09:56:38: 8000000 INFO @ Fri, 10 Dec 2021 09:56:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8574277/SRX8574277.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8574277/SRX8574277.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8574277/SRX8574277.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8574277/SRX8574277.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, 10 Dec 2021 09:56:38: #1 read tag files... INFO @ Fri, 10 Dec 2021 09:56:38: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 09:56:45: 5000000 INFO @ Fri, 10 Dec 2021 09:56:46: 1000000 INFO @ Fri, 10 Dec 2021 09:56:46: 9000000 INFO @ Fri, 10 Dec 2021 09:56:52: 6000000 INFO @ Fri, 10 Dec 2021 09:56:53: 2000000 INFO @ Fri, 10 Dec 2021 09:56:54: 10000000 INFO @ Fri, 10 Dec 2021 09:56:59: 7000000 INFO @ Fri, 10 Dec 2021 09:57:01: 3000000 INFO @ Fri, 10 Dec 2021 09:57:02: 11000000 INFO @ Fri, 10 Dec 2021 09:57:07: 8000000 INFO @ Fri, 10 Dec 2021 09:57:09: 4000000 INFO @ Fri, 10 Dec 2021 09:57:09: 12000000 INFO @ Fri, 10 Dec 2021 09:57:14: 9000000 INFO @ Fri, 10 Dec 2021 09:57:16: 5000000 INFO @ Fri, 10 Dec 2021 09:57:17: 13000000 INFO @ Fri, 10 Dec 2021 09:57:21: 10000000 INFO @ Fri, 10 Dec 2021 09:57:24: 6000000 INFO @ Fri, 10 Dec 2021 09:57:25: 14000000 INFO @ Fri, 10 Dec 2021 09:57:28: 11000000 INFO @ Fri, 10 Dec 2021 09:57:31: 7000000 INFO @ Fri, 10 Dec 2021 09:57:32: 15000000 INFO @ Fri, 10 Dec 2021 09:57:36: 12000000 INFO @ Fri, 10 Dec 2021 09:57:39: 8000000 INFO @ Fri, 10 Dec 2021 09:57:41: 16000000 INFO @ Fri, 10 Dec 2021 09:57:43: 13000000 INFO @ Fri, 10 Dec 2021 09:57:47: 9000000 INFO @ Fri, 10 Dec 2021 09:57:49: 17000000 INFO @ Fri, 10 Dec 2021 09:57:51: 14000000 INFO @ Fri, 10 Dec 2021 09:57:55: 10000000 INFO @ Fri, 10 Dec 2021 09:57:57: 18000000 INFO @ Fri, 10 Dec 2021 09:57:58: 15000000 INFO @ Fri, 10 Dec 2021 09:58:02: 11000000 INFO @ Fri, 10 Dec 2021 09:58:04: 19000000 INFO @ Fri, 10 Dec 2021 09:58:06: 16000000 INFO @ Fri, 10 Dec 2021 09:58:10: 12000000 INFO @ Fri, 10 Dec 2021 09:58:11: 20000000 INFO @ Fri, 10 Dec 2021 09:58:13: 17000000 INFO @ Fri, 10 Dec 2021 09:58:17: 13000000 INFO @ Fri, 10 Dec 2021 09:58:19: 21000000 INFO @ Fri, 10 Dec 2021 09:58:20: 18000000 INFO @ Fri, 10 Dec 2021 09:58:25: 14000000 INFO @ Fri, 10 Dec 2021 09:58:26: 22000000 INFO @ Fri, 10 Dec 2021 09:58:28: 19000000 INFO @ Fri, 10 Dec 2021 09:58:33: 15000000 INFO @ Fri, 10 Dec 2021 09:58:33: 23000000 INFO @ Fri, 10 Dec 2021 09:58:35: 20000000 INFO @ Fri, 10 Dec 2021 09:58:40: 16000000 INFO @ Fri, 10 Dec 2021 09:58:41: 24000000 INFO @ Fri, 10 Dec 2021 09:58:42: 21000000 INFO @ Fri, 10 Dec 2021 09:58:47: 17000000 INFO @ Fri, 10 Dec 2021 09:58:48: 25000000 INFO @ Fri, 10 Dec 2021 09:58:49: 22000000 INFO @ Fri, 10 Dec 2021 09:58:55: 18000000 INFO @ Fri, 10 Dec 2021 09:58:55: 26000000 INFO @ Fri, 10 Dec 2021 09:58:57: 23000000 INFO @ Fri, 10 Dec 2021 09:59:02: 19000000 INFO @ Fri, 10 Dec 2021 09:59:02: 27000000 INFO @ Fri, 10 Dec 2021 09:59:04: 24000000 INFO @ Fri, 10 Dec 2021 09:59:10: 28000000 INFO @ Fri, 10 Dec 2021 09:59:10: 20000000 INFO @ Fri, 10 Dec 2021 09:59:12: 25000000 INFO @ Fri, 10 Dec 2021 09:59:17: 29000000 INFO @ Fri, 10 Dec 2021 09:59:18: 21000000 INFO @ Fri, 10 Dec 2021 09:59:20: 26000000 INFO @ Fri, 10 Dec 2021 09:59:25: 30000000 INFO @ Fri, 10 Dec 2021 09:59:26: 22000000 INFO @ Fri, 10 Dec 2021 09:59:28: 27000000 INFO @ Fri, 10 Dec 2021 09:59:33: 31000000 INFO @ Fri, 10 Dec 2021 09:59:33: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 09:59:35: 28000000 INFO @ Fri, 10 Dec 2021 09:59:40: 32000000 INFO @ Fri, 10 Dec 2021 09:59:41: 24000000 INFO @ Fri, 10 Dec 2021 09:59:43: 29000000 INFO @ Fri, 10 Dec 2021 09:59:48: 33000000 INFO @ Fri, 10 Dec 2021 09:59:49: 25000000 INFO @ Fri, 10 Dec 2021 09:59:51: 30000000 INFO @ Fri, 10 Dec 2021 09:59:55: 34000000 INFO @ Fri, 10 Dec 2021 09:59:56: 26000000 INFO @ Fri, 10 Dec 2021 09:59:57: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 09:59:57: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 09:59:57: #1 total tags in treatment: 34297334 INFO @ Fri, 10 Dec 2021 09:59:57: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 09:59:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 09:59:58: #1 tags after filtering in treatment: 34297334 INFO @ Fri, 10 Dec 2021 09:59:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 09:59:58: #1 finished! INFO @ Fri, 10 Dec 2021 09:59:58: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 09:59:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 09:59:58: 31000000 INFO @ Fri, 10 Dec 2021 10:00:00: #2 number of paired peaks: 145 WARNING @ Fri, 10 Dec 2021 10:00:00: Fewer paired peaks (145) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 145 pairs to build model! INFO @ Fri, 10 Dec 2021 10:00:00: start model_add_line... INFO @ Fri, 10 Dec 2021 10:00:01: start X-correlation... INFO @ Fri, 10 Dec 2021 10:00:01: end of X-cor INFO @ Fri, 10 Dec 2021 10:00:01: #2 finished! INFO @ Fri, 10 Dec 2021 10:00:01: #2 predicted fragment length is 152 bps INFO @ Fri, 10 Dec 2021 10:00:01: #2 alternative fragment length(s) may be 4,152 bps INFO @ Fri, 10 Dec 2021 10:00:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8574277/SRX8574277.05_model.r INFO @ Fri, 10 Dec 2021 10:00:01: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:00:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:00:03: 27000000 INFO @ Fri, 10 Dec 2021 10:00:05: 32000000 INFO @ Fri, 10 Dec 2021 10:00:10: 28000000 INFO @ Fri, 10 Dec 2021 10:00:12: 33000000 INFO @ Fri, 10 Dec 2021 10:00:18: 29000000 INFO @ Fri, 10 Dec 2021 10:00:20: 34000000 INFO @ Fri, 10 Dec 2021 10:00:22: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 10:00:22: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 10:00:22: #1 total tags in treatment: 34297334 INFO @ Fri, 10 Dec 2021 10:00:22: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:00:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 10:00:23: #1 tags after filtering in treatment: 34297334 INFO @ Fri, 10 Dec 2021 10:00:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 10:00:23: #1 finished! INFO @ Fri, 10 Dec 2021 10:00:23: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:00:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:00:26: 30000000 INFO @ Fri, 10 Dec 2021 10:00:26: #2 number of paired peaks: 145 WARNING @ Fri, 10 Dec 2021 10:00:26: Fewer paired peaks (145) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 145 pairs to build model! INFO @ Fri, 10 Dec 2021 10:00:26: start model_add_line... INFO @ Fri, 10 Dec 2021 10:00:26: start X-correlation... INFO @ Fri, 10 Dec 2021 10:00:26: end of X-cor INFO @ Fri, 10 Dec 2021 10:00:26: #2 finished! INFO @ Fri, 10 Dec 2021 10:00:26: #2 predicted fragment length is 152 bps INFO @ Fri, 10 Dec 2021 10:00:26: #2 alternative fragment length(s) may be 4,152 bps INFO @ Fri, 10 Dec 2021 10:00:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8574277/SRX8574277.10_model.r INFO @ Fri, 10 Dec 2021 10:00:26: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:00:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:00:33: 31000000 INFO @ Fri, 10 Dec 2021 10:00:40: 32000000 INFO @ Fri, 10 Dec 2021 10:00:47: 33000000 INFO @ Fri, 10 Dec 2021 10:00:54: 34000000 INFO @ Fri, 10 Dec 2021 10:00:56: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 10:00:56: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 10:00:56: #1 total tags in treatment: 34297334 INFO @ Fri, 10 Dec 2021 10:00:56: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:00:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 10:00:57: #1 tags after filtering in treatment: 34297334 INFO @ Fri, 10 Dec 2021 10:00:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 10:00:57: #1 finished! INFO @ Fri, 10 Dec 2021 10:00:57: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:00:57: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 10:00:59: #2 number of paired peaks: 145 WARNING @ Fri, 10 Dec 2021 10:00:59: Fewer paired peaks (145) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 145 pairs to build model! INFO @ Fri, 10 Dec 2021 10:00:59: start model_add_line... INFO @ Fri, 10 Dec 2021 10:01:00: start X-correlation... INFO @ Fri, 10 Dec 2021 10:01:00: end of X-cor INFO @ Fri, 10 Dec 2021 10:01:00: #2 finished! INFO @ Fri, 10 Dec 2021 10:01:00: #2 predicted fragment length is 152 bps INFO @ Fri, 10 Dec 2021 10:01:00: #2 alternative fragment length(s) may be 4,152 bps INFO @ Fri, 10 Dec 2021 10:01:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8574277/SRX8574277.20_model.r INFO @ Fri, 10 Dec 2021 10:01:00: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:01:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:01:11: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:01:34: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:01:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8574277/SRX8574277.05_peaks.xls INFO @ Fri, 10 Dec 2021 10:01:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8574277/SRX8574277.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:01:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8574277/SRX8574277.05_summits.bed INFO @ Fri, 10 Dec 2021 10:01:45: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9266 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 10:02:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8574277/SRX8574277.10_peaks.xls INFO @ Fri, 10 Dec 2021 10:02:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8574277/SRX8574277.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:02:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8574277/SRX8574277.10_summits.bed INFO @ Fri, 10 Dec 2021 10:02:08: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6556 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 10:02:12: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:02:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8574277/SRX8574277.20_peaks.xls INFO @ Fri, 10 Dec 2021 10:02:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8574277/SRX8574277.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:02:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8574277/SRX8574277.20_summits.bed INFO @ Fri, 10 Dec 2021 10:02:46: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3845 records, 4 fields): 26 millis CompletedMACS2peakCalling