Job ID = 10166175 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 10166526 ("srTdm6") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:45 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: 00:06:46 Overall time: 00:06:46 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 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:47:09: # 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 @ Thu, 08 Oct 2020 20:47:09: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:47:09: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:47:15: 1000000 INFO @ Thu, 08 Oct 2020 20:47:22: 2000000 INFO @ Thu, 08 Oct 2020 20:47:28: 3000000 INFO @ Thu, 08 Oct 2020 20:47:34: 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 @ Thu, 08 Oct 2020 20:47:39: # 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 @ Thu, 08 Oct 2020 20:47:39: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:47:39: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:47:40: 5000000 INFO @ Thu, 08 Oct 2020 20:47:46: 1000000 INFO @ Thu, 08 Oct 2020 20:47:47: 6000000 INFO @ Thu, 08 Oct 2020 20:47:53: 2000000 INFO @ Thu, 08 Oct 2020 20:47:55: 7000000 INFO @ Thu, 08 Oct 2020 20:48:00: 3000000 INFO @ Thu, 08 Oct 2020 20:48:02: 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 @ Thu, 08 Oct 2020 20:48:07: 4000000 INFO @ Thu, 08 Oct 2020 20:48:09: 9000000 INFO @ Thu, 08 Oct 2020 20:48:09: # 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 @ Thu, 08 Oct 2020 20:48:09: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:48:09: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:48:15: 5000000 INFO @ Thu, 08 Oct 2020 20:48:16: 10000000 INFO @ Thu, 08 Oct 2020 20:48:16: 1000000 INFO @ Thu, 08 Oct 2020 20:48:22: 6000000 INFO @ Thu, 08 Oct 2020 20:48:23: 11000000 INFO @ Thu, 08 Oct 2020 20:48:23: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 20:48:23: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 20:48:23: #1 total tags in treatment: 11036828 INFO @ Thu, 08 Oct 2020 20:48:23: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:48:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:48:23: #1 tags after filtering in treatment: 11036828 INFO @ Thu, 08 Oct 2020 20:48:23: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:48:23: #1 finished! INFO @ Thu, 08 Oct 2020 20:48:23: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:48:23: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:48:24: 2000000 INFO @ Thu, 08 Oct 2020 20:48:25: #2 number of paired peaks: 5134 INFO @ Thu, 08 Oct 2020 20:48:25: start model_add_line... INFO @ Thu, 08 Oct 2020 20:48:25: start X-correlation... INFO @ Thu, 08 Oct 2020 20:48:25: end of X-cor INFO @ Thu, 08 Oct 2020 20:48:25: #2 finished! INFO @ Thu, 08 Oct 2020 20:48:25: #2 predicted fragment length is 127 bps INFO @ Thu, 08 Oct 2020 20:48:25: #2 alternative fragment length(s) may be 127 bps INFO @ Thu, 08 Oct 2020 20:48:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723705/SRX7723705.05_model.r WARNING @ Thu, 08 Oct 2020 20:48:25: #2 Since the d (127) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:48:25: #2 You may need to consider one of the other alternative d(s): 127 WARNING @ Thu, 08 Oct 2020 20:48:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:48:25: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:48:25: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:48:29: 7000000 INFO @ Thu, 08 Oct 2020 20:48:31: 3000000 INFO @ Thu, 08 Oct 2020 20:48:36: 8000000 INFO @ Thu, 08 Oct 2020 20:48:38: 4000000 INFO @ Thu, 08 Oct 2020 20:48:43: 9000000 INFO @ Thu, 08 Oct 2020 20:48:45: 5000000 INFO @ Thu, 08 Oct 2020 20:48:51: 10000000 INFO @ Thu, 08 Oct 2020 20:48:51: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:48:53: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:48:58: 11000000 INFO @ Thu, 08 Oct 2020 20:48:58: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 20:48:58: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 20:48:58: #1 total tags in treatment: 11036828 INFO @ Thu, 08 Oct 2020 20:48:58: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:48:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:48:58: #1 tags after filtering in treatment: 11036828 INFO @ Thu, 08 Oct 2020 20:48:58: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:48:58: #1 finished! INFO @ Thu, 08 Oct 2020 20:48:58: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:48:58: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:48:59: #2 number of paired peaks: 5134 INFO @ Thu, 08 Oct 2020 20:48:59: start model_add_line... INFO @ Thu, 08 Oct 2020 20:48:59: start X-correlation... INFO @ Thu, 08 Oct 2020 20:48:59: end of X-cor INFO @ Thu, 08 Oct 2020 20:48:59: #2 finished! INFO @ Thu, 08 Oct 2020 20:48:59: #2 predicted fragment length is 127 bps INFO @ Thu, 08 Oct 2020 20:48:59: #2 alternative fragment length(s) may be 127 bps INFO @ Thu, 08 Oct 2020 20:48:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723705/SRX7723705.10_model.r WARNING @ Thu, 08 Oct 2020 20:48:59: #2 Since the d (127) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:48:59: #2 You may need to consider one of the other alternative d(s): 127 WARNING @ Thu, 08 Oct 2020 20:48:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:48:59: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:48:59: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:49:00: 7000000 INFO @ Thu, 08 Oct 2020 20:49:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723705/SRX7723705.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:49:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723705/SRX7723705.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:49:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723705/SRX7723705.05_summits.bed INFO @ Thu, 08 Oct 2020 20:49:05: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (24895 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:49:06: 8000000 INFO @ Thu, 08 Oct 2020 20:49:13: 9000000 BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:49:20: 10000000 INFO @ Thu, 08 Oct 2020 20:49:25: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:49:26: 11000000 INFO @ Thu, 08 Oct 2020 20:49:26: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 20:49:26: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 20:49:26: #1 total tags in treatment: 11036828 INFO @ Thu, 08 Oct 2020 20:49:26: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:49:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:49:26: #1 tags after filtering in treatment: 11036828 INFO @ Thu, 08 Oct 2020 20:49:26: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:49:26: #1 finished! INFO @ Thu, 08 Oct 2020 20:49:26: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:49:26: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:49:27: #2 number of paired peaks: 5134 INFO @ Thu, 08 Oct 2020 20:49:27: start model_add_line... INFO @ Thu, 08 Oct 2020 20:49:28: start X-correlation... INFO @ Thu, 08 Oct 2020 20:49:28: end of X-cor INFO @ Thu, 08 Oct 2020 20:49:28: #2 finished! INFO @ Thu, 08 Oct 2020 20:49:28: #2 predicted fragment length is 127 bps INFO @ Thu, 08 Oct 2020 20:49:28: #2 alternative fragment length(s) may be 127 bps INFO @ Thu, 08 Oct 2020 20:49:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723705/SRX7723705.20_model.r WARNING @ Thu, 08 Oct 2020 20:49:28: #2 Since the d (127) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:49:28: #2 You may need to consider one of the other alternative d(s): 127 WARNING @ Thu, 08 Oct 2020 20:49:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:49:28: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:49:28: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:49:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723705/SRX7723705.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:49:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723705/SRX7723705.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:49:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723705/SRX7723705.10_summits.bed INFO @ Thu, 08 Oct 2020 20:49:39: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (18065 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:49:54: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:50:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723705/SRX7723705.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:50:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723705/SRX7723705.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:50:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723705/SRX7723705.20_summits.bed INFO @ Thu, 08 Oct 2020 20:50:08: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (11372 records, 4 fields): 25 millis CompletedMACS2peakCalling