Job ID = 14166967 SRX = SRX7723705 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 22464182 spots for SRR11084661/SRR11084661.sra Written 22464182 spots for SRR11084661/SRR11084661.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167299 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:09:59 22464182 reads; of these: 22464182 (100.00%) were unpaired; of these: 4248324 (18.91%) aligned 0 times 16577987 (73.80%) aligned exactly 1 time 1637871 (7.29%) aligned >1 times 81.09% overall alignment rate Time searching: 00:10:00 Overall time: 00:10:01 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 8 files... [bam_rmdupse_core] 7179030 / 18215858 = 0.3941 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 08:31:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723705/SRX7723705.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723705/SRX7723705.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723705/SRX7723705.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723705/SRX7723705.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 08:31:13: #1 read tag files... INFO @ Fri, 10 Dec 2021 08:31:13: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 08:31:24: 1000000 INFO @ Fri, 10 Dec 2021 08:31:34: 2000000 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 08:31:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723705/SRX7723705.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723705/SRX7723705.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723705/SRX7723705.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723705/SRX7723705.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 08:31:42: #1 read tag files... INFO @ Fri, 10 Dec 2021 08:31:42: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 08:31:45: 3000000 INFO @ Fri, 10 Dec 2021 08:31:54: 1000000 INFO @ Fri, 10 Dec 2021 08:31:56: 4000000 INFO @ Fri, 10 Dec 2021 08:32:05: 2000000 INFO @ Fri, 10 Dec 2021 08:32:08: 5000000 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 08:32:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723705/SRX7723705.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723705/SRX7723705.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723705/SRX7723705.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723705/SRX7723705.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 08:32:12: #1 read tag files... INFO @ Fri, 10 Dec 2021 08:32:12: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 08:32:16: 3000000 INFO @ Fri, 10 Dec 2021 08:32:19: 6000000 INFO @ Fri, 10 Dec 2021 08:32:24: 1000000 INFO @ Fri, 10 Dec 2021 08:32:28: 4000000 INFO @ Fri, 10 Dec 2021 08:32:31: 7000000 INFO @ Fri, 10 Dec 2021 08:32:36: 2000000 INFO @ Fri, 10 Dec 2021 08:32:40: 5000000 INFO @ Fri, 10 Dec 2021 08:32:42: 8000000 INFO @ Fri, 10 Dec 2021 08:32:47: 3000000 INFO @ Fri, 10 Dec 2021 08:32:51: 6000000 INFO @ Fri, 10 Dec 2021 08:32:53: 9000000 INFO @ Fri, 10 Dec 2021 08:32:59: 4000000 INFO @ Fri, 10 Dec 2021 08:33:03: 7000000 INFO @ Fri, 10 Dec 2021 08:33:05: 10000000 INFO @ Fri, 10 Dec 2021 08:33:10: 5000000 INFO @ Fri, 10 Dec 2021 08:33:15: 8000000 INFO @ Fri, 10 Dec 2021 08:33:17: 11000000 INFO @ Fri, 10 Dec 2021 08:33:18: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 08:33:18: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 08:33:18: #1 total tags in treatment: 11036828 INFO @ Fri, 10 Dec 2021 08:33:18: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 08:33:18: #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 08:33:18: #1 tags after filtering in treatment: 11036828 INFO @ Fri, 10 Dec 2021 08:33:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 08:33:18: #1 finished! INFO @ Fri, 10 Dec 2021 08:33:18: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 08:33:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 08:33:19: #2 number of paired peaks: 5134 INFO @ Fri, 10 Dec 2021 08:33:19: start model_add_line... INFO @ Fri, 10 Dec 2021 08:33:20: start X-correlation... INFO @ Fri, 10 Dec 2021 08:33:20: end of X-cor INFO @ Fri, 10 Dec 2021 08:33:20: #2 finished! INFO @ Fri, 10 Dec 2021 08:33:20: #2 predicted fragment length is 127 bps INFO @ Fri, 10 Dec 2021 08:33:20: #2 alternative fragment length(s) may be 127 bps INFO @ Fri, 10 Dec 2021 08:33:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723705/SRX7723705.05_model.r WARNING @ Fri, 10 Dec 2021 08:33:20: #2 Since the d (127) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 08:33:20: #2 You may need to consider one of the other alternative d(s): 127 WARNING @ Fri, 10 Dec 2021 08:33:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 08:33:20: #3 Call peaks... INFO @ Fri, 10 Dec 2021 08:33:20: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 08:33:22: 6000000 INFO @ Fri, 10 Dec 2021 08:33:26: 9000000 INFO @ Fri, 10 Dec 2021 08:33:33: 7000000 INFO @ Fri, 10 Dec 2021 08:33:37: 10000000 INFO @ Fri, 10 Dec 2021 08:33:44: 8000000 INFO @ Fri, 10 Dec 2021 08:33:48: 11000000 INFO @ Fri, 10 Dec 2021 08:33:49: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 08:33:49: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 08:33:49: #1 total tags in treatment: 11036828 INFO @ Fri, 10 Dec 2021 08:33:49: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 08:33:49: #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 08:33:49: #1 tags after filtering in treatment: 11036828 INFO @ Fri, 10 Dec 2021 08:33:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 08:33:49: #1 finished! INFO @ Fri, 10 Dec 2021 08:33:49: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 08:33:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 08:33:51: #2 number of paired peaks: 5134 INFO @ Fri, 10 Dec 2021 08:33:51: start model_add_line... INFO @ Fri, 10 Dec 2021 08:33:51: start X-correlation... INFO @ Fri, 10 Dec 2021 08:33:51: end of X-cor INFO @ Fri, 10 Dec 2021 08:33:51: #2 finished! INFO @ Fri, 10 Dec 2021 08:33:51: #2 predicted fragment length is 127 bps INFO @ Fri, 10 Dec 2021 08:33:51: #2 alternative fragment length(s) may be 127 bps INFO @ Fri, 10 Dec 2021 08:33:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723705/SRX7723705.10_model.r WARNING @ Fri, 10 Dec 2021 08:33:51: #2 Since the d (127) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 08:33:51: #2 You may need to consider one of the other alternative d(s): 127 WARNING @ Fri, 10 Dec 2021 08:33:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 08:33:51: #3 Call peaks... INFO @ Fri, 10 Dec 2021 08:33:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 08:33:54: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 08:33:55: 9000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 08:34:06: 10000000 INFO @ Fri, 10 Dec 2021 08:34:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723705/SRX7723705.05_peaks.xls INFO @ Fri, 10 Dec 2021 08:34:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723705/SRX7723705.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 08:34:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723705/SRX7723705.05_summits.bed INFO @ Fri, 10 Dec 2021 08:34:13: Done! pass1 - making usageList (15 chroms): 8 millis pass2 - checking and writing primary data (24895 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 08:34:17: 11000000 INFO @ Fri, 10 Dec 2021 08:34:17: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 08:34:17: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 08:34:17: #1 total tags in treatment: 11036828 INFO @ Fri, 10 Dec 2021 08:34:17: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 08:34:17: #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 08:34:18: #1 tags after filtering in treatment: 11036828 INFO @ Fri, 10 Dec 2021 08:34:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 08:34:18: #1 finished! INFO @ Fri, 10 Dec 2021 08:34:18: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 08:34:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 08:34:19: #2 number of paired peaks: 5134 INFO @ Fri, 10 Dec 2021 08:34:19: start model_add_line... INFO @ Fri, 10 Dec 2021 08:34:19: start X-correlation... INFO @ Fri, 10 Dec 2021 08:34:19: end of X-cor INFO @ Fri, 10 Dec 2021 08:34:19: #2 finished! INFO @ Fri, 10 Dec 2021 08:34:19: #2 predicted fragment length is 127 bps INFO @ Fri, 10 Dec 2021 08:34:19: #2 alternative fragment length(s) may be 127 bps INFO @ Fri, 10 Dec 2021 08:34:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723705/SRX7723705.20_model.r WARNING @ Fri, 10 Dec 2021 08:34:19: #2 Since the d (127) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 08:34:19: #2 You may need to consider one of the other alternative d(s): 127 WARNING @ Fri, 10 Dec 2021 08:34:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 08:34:19: #3 Call peaks... INFO @ Fri, 10 Dec 2021 08:34:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 08:34:25: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 08:34:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723705/SRX7723705.10_peaks.xls INFO @ Fri, 10 Dec 2021 08:34:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723705/SRX7723705.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 08:34:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723705/SRX7723705.10_summits.bed INFO @ Fri, 10 Dec 2021 08:34:43: Done! pass1 - making usageList (14 chroms): 7 millis pass2 - checking and writing primary data (18065 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 08:34:55: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 08:35:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723705/SRX7723705.20_peaks.xls INFO @ Fri, 10 Dec 2021 08:35:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723705/SRX7723705.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 08:35:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723705/SRX7723705.20_summits.bed INFO @ Fri, 10 Dec 2021 08:35:13: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (11372 records, 4 fields): 17 millis CompletedMACS2peakCalling