Job ID = 12264878 SRX = SRX3032277 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 7664058 spots for SRR5863967/SRR5863967.sra Written 7664058 spots for SRR5863967/SRR5863967.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265031 ("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: 00:02:54 7664058 reads; of these: 7664058 (100.00%) were unpaired; of these: 2289111 (29.87%) aligned 0 times 4529346 (59.10%) aligned exactly 1 time 845601 (11.03%) aligned >1 times 70.13% overall alignment rate Time searching: 00:02:54 Overall time: 00:02:54 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_rmdupse_core] 1522016 / 5374947 = 0.2832 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 05:59:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032277/SRX3032277.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032277/SRX3032277.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032277/SRX3032277.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032277/SRX3032277.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 05:59:37: #1 read tag files... INFO @ Sat, 03 Apr 2021 05:59:37: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 05:59:48: 1000000 INFO @ Sat, 03 Apr 2021 05:59:58: 2000000 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 06:00:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032277/SRX3032277.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032277/SRX3032277.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032277/SRX3032277.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032277/SRX3032277.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 06:00:07: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:00:07: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:00:08: 3000000 INFO @ Sat, 03 Apr 2021 06:00:17: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 06:00:17: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 06:00:17: #1 total tags in treatment: 3852931 INFO @ Sat, 03 Apr 2021 06:00:17: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:00:17: #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 06:00:17: #1 tags after filtering in treatment: 3852931 INFO @ Sat, 03 Apr 2021 06:00:17: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:00:17: #1 finished! INFO @ Sat, 03 Apr 2021 06:00:17: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:00:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:00:17: #2 number of paired peaks: 5184 INFO @ Sat, 03 Apr 2021 06:00:17: start model_add_line... INFO @ Sat, 03 Apr 2021 06:00:17: start X-correlation... INFO @ Sat, 03 Apr 2021 06:00:17: end of X-cor INFO @ Sat, 03 Apr 2021 06:00:17: #2 finished! INFO @ Sat, 03 Apr 2021 06:00:17: #2 predicted fragment length is 109 bps INFO @ Sat, 03 Apr 2021 06:00:17: #2 alternative fragment length(s) may be 109 bps INFO @ Sat, 03 Apr 2021 06:00:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032277/SRX3032277.05_model.r WARNING @ Sat, 03 Apr 2021 06:00:17: #2 Since the d (109) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:00:17: #2 You may need to consider one of the other alternative d(s): 109 WARNING @ Sat, 03 Apr 2021 06:00:17: #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 06:00:17: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:00:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:00:21: 1000000 INFO @ Sat, 03 Apr 2021 06:00:30: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:00:35: 2000000 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 06:00:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032277/SRX3032277.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:00:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032277/SRX3032277.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:00:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032277/SRX3032277.05_summits.bed INFO @ Sat, 03 Apr 2021 06:00:37: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (12199 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:00:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032277/SRX3032277.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032277/SRX3032277.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032277/SRX3032277.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032277/SRX3032277.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 06:00:37: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:00:37: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:00:48: 3000000 INFO @ Sat, 03 Apr 2021 06:00:48: 1000000 INFO @ Sat, 03 Apr 2021 06:00:58: 2000000 INFO @ Sat, 03 Apr 2021 06:00:59: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 06:00:59: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 06:00:59: #1 total tags in treatment: 3852931 INFO @ Sat, 03 Apr 2021 06:00:59: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:00:59: #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 06:00:59: #1 tags after filtering in treatment: 3852931 INFO @ Sat, 03 Apr 2021 06:00:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:00:59: #1 finished! INFO @ Sat, 03 Apr 2021 06:00:59: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:00:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:01:00: #2 number of paired peaks: 5184 INFO @ Sat, 03 Apr 2021 06:01:00: start model_add_line... INFO @ Sat, 03 Apr 2021 06:01:00: start X-correlation... INFO @ Sat, 03 Apr 2021 06:01:00: end of X-cor INFO @ Sat, 03 Apr 2021 06:01:00: #2 finished! INFO @ Sat, 03 Apr 2021 06:01:00: #2 predicted fragment length is 109 bps INFO @ Sat, 03 Apr 2021 06:01:00: #2 alternative fragment length(s) may be 109 bps INFO @ Sat, 03 Apr 2021 06:01:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032277/SRX3032277.10_model.r WARNING @ Sat, 03 Apr 2021 06:01:00: #2 Since the d (109) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:01:00: #2 You may need to consider one of the other alternative d(s): 109 WARNING @ Sat, 03 Apr 2021 06:01:00: #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 06:01:00: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:01:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:01:08: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:01:12: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:01:16: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 06:01:16: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 06:01:16: #1 total tags in treatment: 3852931 INFO @ Sat, 03 Apr 2021 06:01:16: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:01:16: #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 06:01:16: #1 tags after filtering in treatment: 3852931 INFO @ Sat, 03 Apr 2021 06:01:16: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:01:16: #1 finished! INFO @ Sat, 03 Apr 2021 06:01:16: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:01:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:01:16: #2 number of paired peaks: 5184 INFO @ Sat, 03 Apr 2021 06:01:16: start model_add_line... INFO @ Sat, 03 Apr 2021 06:01:16: start X-correlation... INFO @ Sat, 03 Apr 2021 06:01:16: end of X-cor INFO @ Sat, 03 Apr 2021 06:01:16: #2 finished! INFO @ Sat, 03 Apr 2021 06:01:16: #2 predicted fragment length is 109 bps INFO @ Sat, 03 Apr 2021 06:01:16: #2 alternative fragment length(s) may be 109 bps INFO @ Sat, 03 Apr 2021 06:01:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032277/SRX3032277.20_model.r WARNING @ Sat, 03 Apr 2021 06:01:16: #2 Since the d (109) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:01:16: #2 You may need to consider one of the other alternative d(s): 109 WARNING @ Sat, 03 Apr 2021 06:01:16: #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 06:01:16: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:01:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:01:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032277/SRX3032277.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:01:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032277/SRX3032277.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:01:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032277/SRX3032277.10_summits.bed INFO @ Sat, 03 Apr 2021 06:01:19: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (6912 records, 4 fields): 24 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:01:28: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:01:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032277/SRX3032277.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:01:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032277/SRX3032277.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:01:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032277/SRX3032277.20_summits.bed INFO @ Sat, 03 Apr 2021 06:01:35: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (2298 records, 4 fields): 6 millis CompletedMACS2peakCalling