Job ID = 12265285 SRX = SRX5010744 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 52695324 spots for SRR8191169/SRR8191169.sra Written 52695324 spots for SRR8191169/SRR8191169.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265451 ("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: 00:11:06 52695324 reads; of these: 52695324 (100.00%) were unpaired; of these: 1250238 (2.37%) aligned 0 times 17831191 (33.84%) aligned exactly 1 time 33613895 (63.79%) aligned >1 times 97.63% overall alignment rate Time searching: 00:11:06 Overall time: 00:11:06 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 24 files... [bam_rmdupse_core] 36657846 / 51445086 = 0.7126 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:44:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5010744/SRX5010744.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5010744/SRX5010744.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5010744/SRX5010744.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5010744/SRX5010744.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, 03 Apr 2021 06:44:47: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:44:47: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:44:52: 1000000 INFO @ Sat, 03 Apr 2021 06:44:57: 2000000 INFO @ Sat, 03 Apr 2021 06:45:01: 3000000 INFO @ Sat, 03 Apr 2021 06:45:06: 4000000 INFO @ Sat, 03 Apr 2021 06:45:11: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:45:16: 6000000 INFO @ Sat, 03 Apr 2021 06:45:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5010744/SRX5010744.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5010744/SRX5010744.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5010744/SRX5010744.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5010744/SRX5010744.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, 03 Apr 2021 06:45:17: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:45:17: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:45:21: 7000000 INFO @ Sat, 03 Apr 2021 06:45:22: 1000000 INFO @ Sat, 03 Apr 2021 06:45:26: 8000000 INFO @ Sat, 03 Apr 2021 06:45:27: 2000000 INFO @ Sat, 03 Apr 2021 06:45:30: 9000000 INFO @ Sat, 03 Apr 2021 06:45:32: 3000000 INFO @ Sat, 03 Apr 2021 06:45:35: 10000000 INFO @ Sat, 03 Apr 2021 06:45:37: 4000000 INFO @ Sat, 03 Apr 2021 06:45:40: 11000000 INFO @ Sat, 03 Apr 2021 06:45:42: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:45:45: 12000000 INFO @ Sat, 03 Apr 2021 06:45:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5010744/SRX5010744.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5010744/SRX5010744.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5010744/SRX5010744.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5010744/SRX5010744.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, 03 Apr 2021 06:45:47: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:45:47: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:45:47: 6000000 INFO @ Sat, 03 Apr 2021 06:45:51: 13000000 INFO @ Sat, 03 Apr 2021 06:45:52: 7000000 INFO @ Sat, 03 Apr 2021 06:45:53: 1000000 INFO @ Sat, 03 Apr 2021 06:45:56: 14000000 INFO @ Sat, 03 Apr 2021 06:45:57: 8000000 INFO @ Sat, 03 Apr 2021 06:45:58: 2000000 INFO @ Sat, 03 Apr 2021 06:46:00: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:46:00: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:46:00: #1 total tags in treatment: 14787240 INFO @ Sat, 03 Apr 2021 06:46:00: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:46:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:46:00: #1 tags after filtering in treatment: 14787240 INFO @ Sat, 03 Apr 2021 06:46:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:46:00: #1 finished! INFO @ Sat, 03 Apr 2021 06:46:00: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:46:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:46:01: #2 number of paired peaks: 339 WARNING @ Sat, 03 Apr 2021 06:46:01: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Sat, 03 Apr 2021 06:46:01: start model_add_line... INFO @ Sat, 03 Apr 2021 06:46:01: start X-correlation... INFO @ Sat, 03 Apr 2021 06:46:01: end of X-cor INFO @ Sat, 03 Apr 2021 06:46:01: #2 finished! INFO @ Sat, 03 Apr 2021 06:46:01: #2 predicted fragment length is 57 bps INFO @ Sat, 03 Apr 2021 06:46:01: #2 alternative fragment length(s) may be 4,57 bps INFO @ Sat, 03 Apr 2021 06:46:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5010744/SRX5010744.05_model.r WARNING @ Sat, 03 Apr 2021 06:46:01: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:46:01: #2 You may need to consider one of the other alternative d(s): 4,57 WARNING @ Sat, 03 Apr 2021 06:46:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:46:01: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:46:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:46:02: 9000000 INFO @ Sat, 03 Apr 2021 06:46:03: 3000000 INFO @ Sat, 03 Apr 2021 06:46:08: 10000000 INFO @ Sat, 03 Apr 2021 06:46:08: 4000000 INFO @ Sat, 03 Apr 2021 06:46:13: 11000000 INFO @ Sat, 03 Apr 2021 06:46:13: 5000000 INFO @ Sat, 03 Apr 2021 06:46:18: 12000000 INFO @ Sat, 03 Apr 2021 06:46:18: 6000000 INFO @ Sat, 03 Apr 2021 06:46:23: 13000000 INFO @ Sat, 03 Apr 2021 06:46:23: 7000000 INFO @ Sat, 03 Apr 2021 06:46:28: 14000000 INFO @ Sat, 03 Apr 2021 06:46:28: 8000000 INFO @ Sat, 03 Apr 2021 06:46:32: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:46:32: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:46:32: #1 total tags in treatment: 14787240 INFO @ Sat, 03 Apr 2021 06:46:32: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:46:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:46:32: #1 tags after filtering in treatment: 14787240 INFO @ Sat, 03 Apr 2021 06:46:32: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:46:32: #1 finished! INFO @ Sat, 03 Apr 2021 06:46:32: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:46:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:46:33: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:46:33: #2 number of paired peaks: 339 WARNING @ Sat, 03 Apr 2021 06:46:33: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Sat, 03 Apr 2021 06:46:33: start model_add_line... INFO @ Sat, 03 Apr 2021 06:46:33: start X-correlation... INFO @ Sat, 03 Apr 2021 06:46:33: end of X-cor INFO @ Sat, 03 Apr 2021 06:46:33: #2 finished! INFO @ Sat, 03 Apr 2021 06:46:33: #2 predicted fragment length is 57 bps INFO @ Sat, 03 Apr 2021 06:46:33: #2 alternative fragment length(s) may be 4,57 bps INFO @ Sat, 03 Apr 2021 06:46:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5010744/SRX5010744.10_model.r WARNING @ Sat, 03 Apr 2021 06:46:33: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:46:33: #2 You may need to consider one of the other alternative d(s): 4,57 WARNING @ Sat, 03 Apr 2021 06:46:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:46:33: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:46:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:46:33: 9000000 INFO @ Sat, 03 Apr 2021 06:46:38: 10000000 INFO @ Sat, 03 Apr 2021 06:46:43: 11000000 INFO @ Sat, 03 Apr 2021 06:46:48: 12000000 INFO @ Sat, 03 Apr 2021 06:46:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5010744/SRX5010744.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:46:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5010744/SRX5010744.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:46:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5010744/SRX5010744.05_summits.bed INFO @ Sat, 03 Apr 2021 06:46:50: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (11298 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:46:53: 13000000 INFO @ Sat, 03 Apr 2021 06:46:58: 14000000 INFO @ Sat, 03 Apr 2021 06:47:02: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:47:02: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:47:02: #1 total tags in treatment: 14787240 INFO @ Sat, 03 Apr 2021 06:47:02: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:47:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:47:02: #1 tags after filtering in treatment: 14787240 INFO @ Sat, 03 Apr 2021 06:47:02: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:47:02: #1 finished! INFO @ Sat, 03 Apr 2021 06:47:02: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:47:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:47:04: #2 number of paired peaks: 339 WARNING @ Sat, 03 Apr 2021 06:47:04: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Sat, 03 Apr 2021 06:47:04: start model_add_line... INFO @ Sat, 03 Apr 2021 06:47:04: start X-correlation... INFO @ Sat, 03 Apr 2021 06:47:04: end of X-cor INFO @ Sat, 03 Apr 2021 06:47:04: #2 finished! INFO @ Sat, 03 Apr 2021 06:47:04: #2 predicted fragment length is 57 bps INFO @ Sat, 03 Apr 2021 06:47:04: #2 alternative fragment length(s) may be 4,57 bps INFO @ Sat, 03 Apr 2021 06:47:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5010744/SRX5010744.20_model.r WARNING @ Sat, 03 Apr 2021 06:47:04: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:47:04: #2 You may need to consider one of the other alternative d(s): 4,57 WARNING @ Sat, 03 Apr 2021 06:47:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:47:04: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:47:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:47:06: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:47:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5010744/SRX5010744.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:47:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5010744/SRX5010744.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:47:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5010744/SRX5010744.10_summits.bed INFO @ Sat, 03 Apr 2021 06:47:24: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5198 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:47:35: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:47:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5010744/SRX5010744.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:47:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5010744/SRX5010744.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:47:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5010744/SRX5010744.20_summits.bed INFO @ Sat, 03 Apr 2021 06:47:51: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (961 records, 4 fields): 3 millis CompletedMACS2peakCalling