Job ID = 14167030 SRX = SRX8574265 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 53469092 spots for SRR12045586/SRR12045586.sra Written 53469092 spots for SRR12045586/SRR12045586.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167407 ("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: 00:15:45 53469092 reads; of these: 53469092 (100.00%) were unpaired; of these: 8682342 (16.24%) aligned 0 times 30662968 (57.35%) aligned exactly 1 time 14123782 (26.41%) aligned >1 times 83.76% overall alignment rate Time searching: 00:15:45 Overall time: 00:15:45 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] 15928113 / 44786750 = 0.3556 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 09:23:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8574265/SRX8574265.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8574265/SRX8574265.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8574265/SRX8574265.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8574265/SRX8574265.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 09:23:49: #1 read tag files... INFO @ Fri, 10 Dec 2021 09:23:49: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 09:23:56: 1000000 INFO @ Fri, 10 Dec 2021 09:24:02: 2000000 INFO @ Fri, 10 Dec 2021 09:24:08: 3000000 INFO @ Fri, 10 Dec 2021 09:24:15: 4000000 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 09:24:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8574265/SRX8574265.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8574265/SRX8574265.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8574265/SRX8574265.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8574265/SRX8574265.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 09:24:19: #1 read tag files... INFO @ Fri, 10 Dec 2021 09:24:19: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 09:24:21: 5000000 INFO @ Fri, 10 Dec 2021 09:24:25: 1000000 INFO @ Fri, 10 Dec 2021 09:24:28: 6000000 INFO @ Fri, 10 Dec 2021 09:24:31: 2000000 INFO @ Fri, 10 Dec 2021 09:24:35: 7000000 INFO @ Fri, 10 Dec 2021 09:24:37: 3000000 INFO @ Fri, 10 Dec 2021 09:24:42: 8000000 INFO @ Fri, 10 Dec 2021 09:24:43: 4000000 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 09:24:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8574265/SRX8574265.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8574265/SRX8574265.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8574265/SRX8574265.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8574265/SRX8574265.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 09:24:49: #1 read tag files... INFO @ Fri, 10 Dec 2021 09:24:49: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 09:24:49: 9000000 INFO @ Fri, 10 Dec 2021 09:24:49: 5000000 INFO @ Fri, 10 Dec 2021 09:24:55: 1000000 INFO @ Fri, 10 Dec 2021 09:24:55: 6000000 INFO @ Fri, 10 Dec 2021 09:24:56: 10000000 INFO @ Fri, 10 Dec 2021 09:25:01: 2000000 INFO @ Fri, 10 Dec 2021 09:25:01: 7000000 INFO @ Fri, 10 Dec 2021 09:25:03: 11000000 INFO @ Fri, 10 Dec 2021 09:25:07: 3000000 INFO @ Fri, 10 Dec 2021 09:25:07: 8000000 INFO @ Fri, 10 Dec 2021 09:25:09: 12000000 INFO @ Fri, 10 Dec 2021 09:25:13: 4000000 INFO @ Fri, 10 Dec 2021 09:25:13: 9000000 INFO @ Fri, 10 Dec 2021 09:25:16: 13000000 INFO @ Fri, 10 Dec 2021 09:25:19: 5000000 INFO @ Fri, 10 Dec 2021 09:25:19: 10000000 INFO @ Fri, 10 Dec 2021 09:25:23: 14000000 INFO @ Fri, 10 Dec 2021 09:25:25: 6000000 INFO @ Fri, 10 Dec 2021 09:25:26: 11000000 INFO @ Fri, 10 Dec 2021 09:25:30: 15000000 INFO @ Fri, 10 Dec 2021 09:25:31: 7000000 INFO @ Fri, 10 Dec 2021 09:25:32: 12000000 INFO @ Fri, 10 Dec 2021 09:25:37: 16000000 INFO @ Fri, 10 Dec 2021 09:25:38: 8000000 INFO @ Fri, 10 Dec 2021 09:25:38: 13000000 INFO @ Fri, 10 Dec 2021 09:25:44: 9000000 INFO @ Fri, 10 Dec 2021 09:25:44: 14000000 INFO @ Fri, 10 Dec 2021 09:25:44: 17000000 INFO @ Fri, 10 Dec 2021 09:25:50: 10000000 INFO @ Fri, 10 Dec 2021 09:25:50: 15000000 INFO @ Fri, 10 Dec 2021 09:25:51: 18000000 INFO @ Fri, 10 Dec 2021 09:25:56: 11000000 INFO @ Fri, 10 Dec 2021 09:25:56: 16000000 INFO @ Fri, 10 Dec 2021 09:25:58: 19000000 INFO @ Fri, 10 Dec 2021 09:26:02: 12000000 INFO @ Fri, 10 Dec 2021 09:26:02: 17000000 INFO @ Fri, 10 Dec 2021 09:26:05: 20000000 INFO @ Fri, 10 Dec 2021 09:26:08: 13000000 INFO @ Fri, 10 Dec 2021 09:26:08: 18000000 INFO @ Fri, 10 Dec 2021 09:26:12: 21000000 INFO @ Fri, 10 Dec 2021 09:26:14: 14000000 INFO @ Fri, 10 Dec 2021 09:26:14: 19000000 INFO @ Fri, 10 Dec 2021 09:26:19: 22000000 INFO @ Fri, 10 Dec 2021 09:26:20: 15000000 INFO @ Fri, 10 Dec 2021 09:26:20: 20000000 INFO @ Fri, 10 Dec 2021 09:26:26: 23000000 INFO @ Fri, 10 Dec 2021 09:26:26: 16000000 INFO @ Fri, 10 Dec 2021 09:26:27: 21000000 INFO @ Fri, 10 Dec 2021 09:26:32: 17000000 INFO @ Fri, 10 Dec 2021 09:26:33: 22000000 INFO @ Fri, 10 Dec 2021 09:26:33: 24000000 INFO @ Fri, 10 Dec 2021 09:26:38: 18000000 INFO @ Fri, 10 Dec 2021 09:26:39: 23000000 INFO @ Fri, 10 Dec 2021 09:26:40: 25000000 INFO @ Fri, 10 Dec 2021 09:26:44: 19000000 INFO @ Fri, 10 Dec 2021 09:26:45: 24000000 INFO @ Fri, 10 Dec 2021 09:26:47: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 09:26:50: 20000000 INFO @ Fri, 10 Dec 2021 09:26:51: 25000000 INFO @ Fri, 10 Dec 2021 09:26:54: 27000000 INFO @ Fri, 10 Dec 2021 09:26:57: 21000000 INFO @ Fri, 10 Dec 2021 09:26:57: 26000000 INFO @ Fri, 10 Dec 2021 09:27:00: 28000000 INFO @ Fri, 10 Dec 2021 09:27:03: 22000000 INFO @ Fri, 10 Dec 2021 09:27:03: 27000000 INFO @ Fri, 10 Dec 2021 09:27:06: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 09:27:06: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 09:27:06: #1 total tags in treatment: 28858637 INFO @ Fri, 10 Dec 2021 09:27:06: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 09:27:06: #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 09:27:07: #1 tags after filtering in treatment: 28858637 INFO @ Fri, 10 Dec 2021 09:27:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 09:27:07: #1 finished! INFO @ Fri, 10 Dec 2021 09:27:07: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 09:27:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 09:27:09: #2 number of paired peaks: 422 WARNING @ Fri, 10 Dec 2021 09:27:09: Fewer paired peaks (422) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 422 pairs to build model! INFO @ Fri, 10 Dec 2021 09:27:09: start model_add_line... INFO @ Fri, 10 Dec 2021 09:27:09: 23000000 INFO @ Fri, 10 Dec 2021 09:27:09: start X-correlation... INFO @ Fri, 10 Dec 2021 09:27:09: end of X-cor INFO @ Fri, 10 Dec 2021 09:27:09: #2 finished! INFO @ Fri, 10 Dec 2021 09:27:09: #2 predicted fragment length is 217 bps INFO @ Fri, 10 Dec 2021 09:27:09: #2 alternative fragment length(s) may be 217 bps INFO @ Fri, 10 Dec 2021 09:27:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8574265/SRX8574265.05_model.r INFO @ Fri, 10 Dec 2021 09:27:09: #3 Call peaks... INFO @ Fri, 10 Dec 2021 09:27:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 09:27:09: 28000000 INFO @ Fri, 10 Dec 2021 09:27:14: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 09:27:14: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 09:27:14: #1 total tags in treatment: 28858637 INFO @ Fri, 10 Dec 2021 09:27:14: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 09:27:14: #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 09:27:15: 24000000 INFO @ Fri, 10 Dec 2021 09:27:15: #1 tags after filtering in treatment: 28858637 INFO @ Fri, 10 Dec 2021 09:27:15: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 09:27:15: #1 finished! INFO @ Fri, 10 Dec 2021 09:27:15: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 09:27:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 09:27:17: #2 number of paired peaks: 422 WARNING @ Fri, 10 Dec 2021 09:27:17: Fewer paired peaks (422) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 422 pairs to build model! INFO @ Fri, 10 Dec 2021 09:27:17: start model_add_line... INFO @ Fri, 10 Dec 2021 09:27:17: start X-correlation... INFO @ Fri, 10 Dec 2021 09:27:17: end of X-cor INFO @ Fri, 10 Dec 2021 09:27:17: #2 finished! INFO @ Fri, 10 Dec 2021 09:27:17: #2 predicted fragment length is 217 bps INFO @ Fri, 10 Dec 2021 09:27:17: #2 alternative fragment length(s) may be 217 bps INFO @ Fri, 10 Dec 2021 09:27:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8574265/SRX8574265.10_model.r INFO @ Fri, 10 Dec 2021 09:27:17: #3 Call peaks... INFO @ Fri, 10 Dec 2021 09:27:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 09:27:20: 25000000 INFO @ Fri, 10 Dec 2021 09:27:26: 26000000 INFO @ Fri, 10 Dec 2021 09:27:31: 27000000 INFO @ Fri, 10 Dec 2021 09:27:37: 28000000 INFO @ Fri, 10 Dec 2021 09:27:42: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 09:27:42: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 09:27:42: #1 total tags in treatment: 28858637 INFO @ Fri, 10 Dec 2021 09:27:42: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 09:27:42: #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 09:27:42: #1 tags after filtering in treatment: 28858637 INFO @ Fri, 10 Dec 2021 09:27:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 09:27:42: #1 finished! INFO @ Fri, 10 Dec 2021 09:27:42: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 09:27:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 09:27:44: #2 number of paired peaks: 422 WARNING @ Fri, 10 Dec 2021 09:27:44: Fewer paired peaks (422) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 422 pairs to build model! INFO @ Fri, 10 Dec 2021 09:27:44: start model_add_line... INFO @ Fri, 10 Dec 2021 09:27:44: start X-correlation... INFO @ Fri, 10 Dec 2021 09:27:44: end of X-cor INFO @ Fri, 10 Dec 2021 09:27:44: #2 finished! INFO @ Fri, 10 Dec 2021 09:27:44: #2 predicted fragment length is 217 bps INFO @ Fri, 10 Dec 2021 09:27:44: #2 alternative fragment length(s) may be 217 bps INFO @ Fri, 10 Dec 2021 09:27:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8574265/SRX8574265.20_model.r INFO @ Fri, 10 Dec 2021 09:27:44: #3 Call peaks... INFO @ Fri, 10 Dec 2021 09:27:44: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 09:28:04: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 09:28:11: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 09:28:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8574265/SRX8574265.05_peaks.xls INFO @ Fri, 10 Dec 2021 09:28:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8574265/SRX8574265.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 09:28:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8574265/SRX8574265.05_summits.bed INFO @ Fri, 10 Dec 2021 09:28:29: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5833 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 09:28:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8574265/SRX8574265.10_peaks.xls INFO @ Fri, 10 Dec 2021 09:28:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8574265/SRX8574265.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 09:28:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8574265/SRX8574265.10_summits.bed INFO @ Fri, 10 Dec 2021 09:28:35: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4383 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 09:28:39: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 09:29:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8574265/SRX8574265.20_peaks.xls INFO @ Fri, 10 Dec 2021 09:29:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8574265/SRX8574265.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 09:29:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8574265/SRX8574265.20_summits.bed INFO @ Fri, 10 Dec 2021 09:29:04: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3113 records, 4 fields): 5 millis CompletedMACS2peakCalling