Job ID = 14171285 SRX = SRX9986137 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 34658013 spots for SRR13591556/SRR13591556.sra Written 34658013 spots for SRR13591556/SRR13591556.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171777 ("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: 00:21:46 34658013 reads; of these: 34658013 (100.00%) were unpaired; of these: 1878123 (5.42%) aligned 0 times 6280054 (18.12%) aligned exactly 1 time 26499836 (76.46%) aligned >1 times 94.58% overall alignment rate Time searching: 00:21:46 Overall time: 00:21:46 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_rmdupse_core] 25020971 / 32779890 = 0.7633 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 11:24:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986137/SRX9986137.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986137/SRX9986137.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986137/SRX9986137.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986137/SRX9986137.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 11:24:48: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:24:48: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:24:53: 1000000 INFO @ Sat, 11 Dec 2021 11:24:59: 2000000 INFO @ Sat, 11 Dec 2021 11:25:04: 3000000 INFO @ Sat, 11 Dec 2021 11:25:10: 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 @ Sat, 11 Dec 2021 11:25:16: 5000000 INFO @ Sat, 11 Dec 2021 11:25:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986137/SRX9986137.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986137/SRX9986137.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986137/SRX9986137.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986137/SRX9986137.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 11:25:17: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:25:17: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:25:21: 6000000 INFO @ Sat, 11 Dec 2021 11:25:23: 1000000 INFO @ Sat, 11 Dec 2021 11:25:28: 7000000 INFO @ Sat, 11 Dec 2021 11:25:29: 2000000 INFO @ Sat, 11 Dec 2021 11:25:32: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 11:25:32: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 11:25:32: #1 total tags in treatment: 7758919 INFO @ Sat, 11 Dec 2021 11:25:32: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:25:32: #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 11:25:32: #1 tags after filtering in treatment: 7758919 INFO @ Sat, 11 Dec 2021 11:25:32: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:25:32: #1 finished! INFO @ Sat, 11 Dec 2021 11:25:32: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:25:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:25:33: #2 number of paired peaks: 984 WARNING @ Sat, 11 Dec 2021 11:25:33: Fewer paired peaks (984) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 984 pairs to build model! INFO @ Sat, 11 Dec 2021 11:25:33: start model_add_line... INFO @ Sat, 11 Dec 2021 11:25:33: start X-correlation... INFO @ Sat, 11 Dec 2021 11:25:33: end of X-cor INFO @ Sat, 11 Dec 2021 11:25:33: #2 finished! INFO @ Sat, 11 Dec 2021 11:25:33: #2 predicted fragment length is 142 bps INFO @ Sat, 11 Dec 2021 11:25:33: #2 alternative fragment length(s) may be 142 bps INFO @ Sat, 11 Dec 2021 11:25:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986137/SRX9986137.05_model.r INFO @ Sat, 11 Dec 2021 11:25:33: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:25:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:25:35: 3000000 INFO @ Sat, 11 Dec 2021 11:25:41: 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 @ Sat, 11 Dec 2021 11:25:47: 5000000 INFO @ Sat, 11 Dec 2021 11:25:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986137/SRX9986137.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986137/SRX9986137.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986137/SRX9986137.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986137/SRX9986137.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 11:25:47: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:25:47: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:25:49: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:25:53: 6000000 INFO @ Sat, 11 Dec 2021 11:25:55: 1000000 INFO @ Sat, 11 Dec 2021 11:25:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986137/SRX9986137.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:25:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986137/SRX9986137.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:25:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986137/SRX9986137.05_summits.bed INFO @ Sat, 11 Dec 2021 11:25:58: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5317 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:25:59: 7000000 INFO @ Sat, 11 Dec 2021 11:26:01: 2000000 INFO @ Sat, 11 Dec 2021 11:26:04: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 11:26:04: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 11:26:04: #1 total tags in treatment: 7758919 INFO @ Sat, 11 Dec 2021 11:26:04: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:26:04: #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 11:26:04: #1 tags after filtering in treatment: 7758919 INFO @ Sat, 11 Dec 2021 11:26:04: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:26:04: #1 finished! INFO @ Sat, 11 Dec 2021 11:26:04: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:26:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:26:05: #2 number of paired peaks: 984 WARNING @ Sat, 11 Dec 2021 11:26:05: Fewer paired peaks (984) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 984 pairs to build model! INFO @ Sat, 11 Dec 2021 11:26:05: start model_add_line... INFO @ Sat, 11 Dec 2021 11:26:05: start X-correlation... INFO @ Sat, 11 Dec 2021 11:26:05: end of X-cor INFO @ Sat, 11 Dec 2021 11:26:05: #2 finished! INFO @ Sat, 11 Dec 2021 11:26:05: #2 predicted fragment length is 142 bps INFO @ Sat, 11 Dec 2021 11:26:05: #2 alternative fragment length(s) may be 142 bps INFO @ Sat, 11 Dec 2021 11:26:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986137/SRX9986137.10_model.r INFO @ Sat, 11 Dec 2021 11:26:05: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:26:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:26:08: 3000000 INFO @ Sat, 11 Dec 2021 11:26:13: 4000000 INFO @ Sat, 11 Dec 2021 11:26:19: 5000000 INFO @ Sat, 11 Dec 2021 11:26:21: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:26:24: 6000000 INFO @ Sat, 11 Dec 2021 11:26:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986137/SRX9986137.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:26:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986137/SRX9986137.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:26:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986137/SRX9986137.10_summits.bed INFO @ Sat, 11 Dec 2021 11:26:29: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3054 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:26:30: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:26:34: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 11:26:34: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 11:26:34: #1 total tags in treatment: 7758919 INFO @ Sat, 11 Dec 2021 11:26:34: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:26:34: #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 11:26:34: #1 tags after filtering in treatment: 7758919 INFO @ Sat, 11 Dec 2021 11:26:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:26:34: #1 finished! INFO @ Sat, 11 Dec 2021 11:26:34: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:26:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:26:35: #2 number of paired peaks: 984 WARNING @ Sat, 11 Dec 2021 11:26:35: Fewer paired peaks (984) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 984 pairs to build model! INFO @ Sat, 11 Dec 2021 11:26:35: start model_add_line... INFO @ Sat, 11 Dec 2021 11:26:35: start X-correlation... INFO @ Sat, 11 Dec 2021 11:26:35: end of X-cor INFO @ Sat, 11 Dec 2021 11:26:35: #2 finished! INFO @ Sat, 11 Dec 2021 11:26:35: #2 predicted fragment length is 142 bps INFO @ Sat, 11 Dec 2021 11:26:35: #2 alternative fragment length(s) may be 142 bps INFO @ Sat, 11 Dec 2021 11:26:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986137/SRX9986137.20_model.r INFO @ Sat, 11 Dec 2021 11:26:35: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:26:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:26:52: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:27:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986137/SRX9986137.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:27:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986137/SRX9986137.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:27:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986137/SRX9986137.20_summits.bed INFO @ Sat, 11 Dec 2021 11:27:00: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1440 records, 4 fields): 5 millis CompletedMACS2peakCalling