Job ID = 6457177 SRX = SRX4520671 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:33:40 prefetch.2.10.7: 1) Downloading 'SRR7659069'... 2020-06-21T11:33:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:36:58 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:36:59 prefetch.2.10.7: 'SRR7659069' is valid 2020-06-21T11:36:59 prefetch.2.10.7: 1) 'SRR7659069' was downloaded successfully 2020-06-21T11:36:59 prefetch.2.10.7: 'SRR7659069' has 0 unresolved dependencies Read 10833308 spots for SRR7659069/SRR7659069.sra Written 10833308 spots for SRR7659069/SRR7659069.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:08 10833308 reads; of these: 10833308 (100.00%) were unpaired; of these: 624944 (5.77%) aligned 0 times 6828616 (63.03%) aligned exactly 1 time 3379748 (31.20%) aligned >1 times 94.23% overall alignment rate Time searching: 00:03:08 Overall time: 00:03:08 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1228079 / 10208364 = 0.1203 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 20:43:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4520671/SRX4520671.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4520671/SRX4520671.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4520671/SRX4520671.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4520671/SRX4520671.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 @ Sun, 21 Jun 2020 20:43:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:43:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:44:04: 1000000 INFO @ Sun, 21 Jun 2020 20:44:10: 2000000 INFO @ Sun, 21 Jun 2020 20:44:17: 3000000 INFO @ Sun, 21 Jun 2020 20:44:23: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 20:44:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4520671/SRX4520671.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4520671/SRX4520671.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4520671/SRX4520671.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4520671/SRX4520671.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 @ Sun, 21 Jun 2020 20:44:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:44:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:44:30: 5000000 INFO @ Sun, 21 Jun 2020 20:44:33: 1000000 INFO @ Sun, 21 Jun 2020 20:44:37: 6000000 INFO @ Sun, 21 Jun 2020 20:44:40: 2000000 INFO @ Sun, 21 Jun 2020 20:44:44: 7000000 INFO @ Sun, 21 Jun 2020 20:44:47: 3000000 INFO @ Sun, 21 Jun 2020 20:44:51: 8000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 20:44:54: 4000000 INFO @ Sun, 21 Jun 2020 20:44:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4520671/SRX4520671.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4520671/SRX4520671.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4520671/SRX4520671.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4520671/SRX4520671.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 @ Sun, 21 Jun 2020 20:44:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:44:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:44:58: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:44:58: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:44:58: #1 total tags in treatment: 8980285 INFO @ Sun, 21 Jun 2020 20:44:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:44:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 20:44:59: #1 tags after filtering in treatment: 8980164 INFO @ Sun, 21 Jun 2020 20:44:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:44:59: #1 finished! INFO @ Sun, 21 Jun 2020 20:44:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:44:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:45:00: #2 number of paired peaks: 1561 INFO @ Sun, 21 Jun 2020 20:45:00: start model_add_line... INFO @ Sun, 21 Jun 2020 20:45:00: start X-correlation... INFO @ Sun, 21 Jun 2020 20:45:00: end of X-cor INFO @ Sun, 21 Jun 2020 20:45:00: #2 finished! INFO @ Sun, 21 Jun 2020 20:45:00: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 20:45:00: #2 alternative fragment length(s) may be 3,51,567 bps INFO @ Sun, 21 Jun 2020 20:45:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4520671/SRX4520671.05_model.r WARNING @ Sun, 21 Jun 2020 20:45:00: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:45:00: #2 You may need to consider one of the other alternative d(s): 3,51,567 WARNING @ Sun, 21 Jun 2020 20:45:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 20:45:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:45:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:45:01: 5000000 INFO @ Sun, 21 Jun 2020 20:45:02: 1000000 INFO @ Sun, 21 Jun 2020 20:45:09: 6000000 INFO @ Sun, 21 Jun 2020 20:45:09: 2000000 INFO @ Sun, 21 Jun 2020 20:45:15: 3000000 INFO @ Sun, 21 Jun 2020 20:45:15: 7000000 INFO @ Sun, 21 Jun 2020 20:45:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:45:21: 4000000 INFO @ Sun, 21 Jun 2020 20:45:23: 8000000 INFO @ Sun, 21 Jun 2020 20:45:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4520671/SRX4520671.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:45:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4520671/SRX4520671.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:45:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4520671/SRX4520671.05_summits.bed INFO @ Sun, 21 Jun 2020 20:45:27: Done! pass1 - making usageList (586 chroms): 1 millis pass2 - checking and writing primary data (2602 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:45:27: 5000000 INFO @ Sun, 21 Jun 2020 20:45:30: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:45:30: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:45:30: #1 total tags in treatment: 8980285 INFO @ Sun, 21 Jun 2020 20:45:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:45:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 20:45:30: #1 tags after filtering in treatment: 8980164 INFO @ Sun, 21 Jun 2020 20:45:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:45:30: #1 finished! INFO @ Sun, 21 Jun 2020 20:45:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:45:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:45:31: #2 number of paired peaks: 1561 INFO @ Sun, 21 Jun 2020 20:45:31: start model_add_line... INFO @ Sun, 21 Jun 2020 20:45:31: start X-correlation... INFO @ Sun, 21 Jun 2020 20:45:31: end of X-cor INFO @ Sun, 21 Jun 2020 20:45:31: #2 finished! INFO @ Sun, 21 Jun 2020 20:45:31: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 20:45:31: #2 alternative fragment length(s) may be 3,51,567 bps INFO @ Sun, 21 Jun 2020 20:45:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4520671/SRX4520671.10_model.r WARNING @ Sun, 21 Jun 2020 20:45:31: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:45:31: #2 You may need to consider one of the other alternative d(s): 3,51,567 WARNING @ Sun, 21 Jun 2020 20:45:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 20:45:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:45:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:45:34: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:45:39: 7000000 INFO @ Sun, 21 Jun 2020 20:45:45: 8000000 INFO @ Sun, 21 Jun 2020 20:45:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:45:51: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:45:51: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:45:51: #1 total tags in treatment: 8980285 INFO @ Sun, 21 Jun 2020 20:45:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:45:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 20:45:51: #1 tags after filtering in treatment: 8980164 INFO @ Sun, 21 Jun 2020 20:45:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:45:51: #1 finished! INFO @ Sun, 21 Jun 2020 20:45:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:45:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:45:52: #2 number of paired peaks: 1561 INFO @ Sun, 21 Jun 2020 20:45:52: start model_add_line... INFO @ Sun, 21 Jun 2020 20:45:52: start X-correlation... INFO @ Sun, 21 Jun 2020 20:45:52: end of X-cor INFO @ Sun, 21 Jun 2020 20:45:52: #2 finished! INFO @ Sun, 21 Jun 2020 20:45:52: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 20:45:52: #2 alternative fragment length(s) may be 3,51,567 bps INFO @ Sun, 21 Jun 2020 20:45:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4520671/SRX4520671.20_model.r WARNING @ Sun, 21 Jun 2020 20:45:52: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:45:52: #2 You may need to consider one of the other alternative d(s): 3,51,567 WARNING @ Sun, 21 Jun 2020 20:45:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 20:45:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:45:52: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:45:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4520671/SRX4520671.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:45:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4520671/SRX4520671.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:45:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4520671/SRX4520671.10_summits.bed INFO @ Sun, 21 Jun 2020 20:45:58: Done! pass1 - making usageList (505 chroms): 1 millis pass2 - checking and writing primary data (1712 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:46:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:46:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4520671/SRX4520671.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:46:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4520671/SRX4520671.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:46:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4520671/SRX4520671.20_summits.bed INFO @ Sun, 21 Jun 2020 20:46:19: Done! pass1 - making usageList (277 chroms): 1 millis pass2 - checking and writing primary data (614 records, 4 fields): 8 millis CompletedMACS2peakCalling