Job ID = 12264883 SRX = SRX3032281 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 7738304 spots for SRR5863971/SRR5863971.sra Written 7738304 spots for SRR5863971/SRR5863971.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265043 ("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: 00:03:15 7738304 reads; of these: 7738304 (100.00%) were unpaired; of these: 2073212 (26.79%) aligned 0 times 4964595 (64.16%) aligned exactly 1 time 700497 (9.05%) aligned >1 times 73.21% overall alignment rate Time searching: 00:03:15 Overall time: 00:03:15 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] 1537140 / 5665092 = 0.2713 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 06:00:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032281/SRX3032281.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032281/SRX3032281.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032281/SRX3032281.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032281/SRX3032281.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 06:00:06: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:00:06: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:00:14: 1000000 INFO @ Sat, 03 Apr 2021 06:00:21: 2000000 INFO @ Sat, 03 Apr 2021 06:00:28: 3000000 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 06:00:35: 4000000 INFO @ Sat, 03 Apr 2021 06:00:36: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 06:00:36: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 06:00:36: #1 total tags in treatment: 4127952 INFO @ Sat, 03 Apr 2021 06:00:36: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:00:36: #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 06:00:36: #1 tags after filtering in treatment: 4127952 INFO @ Sat, 03 Apr 2021 06:00:36: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:00:36: #1 finished! INFO @ Sat, 03 Apr 2021 06:00:36: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:00:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:00:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032281/SRX3032281.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032281/SRX3032281.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032281/SRX3032281.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032281/SRX3032281.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 06:00:36: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:00:36: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:00:37: #2 number of paired peaks: 5814 INFO @ Sat, 03 Apr 2021 06:00:37: start model_add_line... INFO @ Sat, 03 Apr 2021 06:00:37: start X-correlation... INFO @ Sat, 03 Apr 2021 06:00:37: end of X-cor INFO @ Sat, 03 Apr 2021 06:00:37: #2 finished! INFO @ Sat, 03 Apr 2021 06:00:37: #2 predicted fragment length is 108 bps INFO @ Sat, 03 Apr 2021 06:00:37: #2 alternative fragment length(s) may be 108 bps INFO @ Sat, 03 Apr 2021 06:00:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032281/SRX3032281.05_model.r WARNING @ Sat, 03 Apr 2021 06:00:37: #2 Since the d (108) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:00:37: #2 You may need to consider one of the other alternative d(s): 108 WARNING @ Sat, 03 Apr 2021 06:00:37: #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 06:00:37: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:00:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:00:44: 1000000 INFO @ Sat, 03 Apr 2021 06:00:49: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:00:52: 2000000 INFO @ Sat, 03 Apr 2021 06:00:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032281/SRX3032281.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:00:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032281/SRX3032281.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:00:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032281/SRX3032281.05_summits.bed INFO @ Sat, 03 Apr 2021 06:00:57: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (13007 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:01:00: 3000000 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 06:01:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032281/SRX3032281.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032281/SRX3032281.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032281/SRX3032281.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032281/SRX3032281.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 06:01:06: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:01:06: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:01:07: 4000000 INFO @ Sat, 03 Apr 2021 06:01:09: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 06:01:09: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 06:01:09: #1 total tags in treatment: 4127952 INFO @ Sat, 03 Apr 2021 06:01:09: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:01:09: #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 06:01:09: #1 tags after filtering in treatment: 4127952 INFO @ Sat, 03 Apr 2021 06:01:09: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:01:09: #1 finished! INFO @ Sat, 03 Apr 2021 06:01:09: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:01:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:01:09: #2 number of paired peaks: 5814 INFO @ Sat, 03 Apr 2021 06:01:09: start model_add_line... INFO @ Sat, 03 Apr 2021 06:01:09: start X-correlation... INFO @ Sat, 03 Apr 2021 06:01:09: end of X-cor INFO @ Sat, 03 Apr 2021 06:01:09: #2 finished! INFO @ Sat, 03 Apr 2021 06:01:09: #2 predicted fragment length is 108 bps INFO @ Sat, 03 Apr 2021 06:01:09: #2 alternative fragment length(s) may be 108 bps INFO @ Sat, 03 Apr 2021 06:01:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032281/SRX3032281.10_model.r WARNING @ Sat, 03 Apr 2021 06:01:09: #2 Since the d (108) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:01:09: #2 You may need to consider one of the other alternative d(s): 108 WARNING @ Sat, 03 Apr 2021 06:01:09: #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 06:01:09: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:01:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:01:15: 1000000 INFO @ Sat, 03 Apr 2021 06:01:22: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:01:23: 2000000 INFO @ Sat, 03 Apr 2021 06:01:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032281/SRX3032281.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:01:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032281/SRX3032281.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:01:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032281/SRX3032281.10_summits.bed INFO @ Sat, 03 Apr 2021 06:01:30: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7926 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:01:31: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:01:38: 4000000 INFO @ Sat, 03 Apr 2021 06:01:39: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 06:01:39: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 06:01:39: #1 total tags in treatment: 4127952 INFO @ Sat, 03 Apr 2021 06:01:39: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:01:39: #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 06:01:39: #1 tags after filtering in treatment: 4127952 INFO @ Sat, 03 Apr 2021 06:01:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:01:39: #1 finished! INFO @ Sat, 03 Apr 2021 06:01:39: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:01:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:01:40: #2 number of paired peaks: 5814 INFO @ Sat, 03 Apr 2021 06:01:40: start model_add_line... INFO @ Sat, 03 Apr 2021 06:01:40: start X-correlation... INFO @ Sat, 03 Apr 2021 06:01:40: end of X-cor INFO @ Sat, 03 Apr 2021 06:01:40: #2 finished! INFO @ Sat, 03 Apr 2021 06:01:40: #2 predicted fragment length is 108 bps INFO @ Sat, 03 Apr 2021 06:01:40: #2 alternative fragment length(s) may be 108 bps INFO @ Sat, 03 Apr 2021 06:01:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032281/SRX3032281.20_model.r WARNING @ Sat, 03 Apr 2021 06:01:40: #2 Since the d (108) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:01:40: #2 You may need to consider one of the other alternative d(s): 108 WARNING @ Sat, 03 Apr 2021 06:01:40: #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 06:01:40: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:01:40: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:01:52: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:01:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032281/SRX3032281.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:01:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032281/SRX3032281.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:01:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032281/SRX3032281.20_summits.bed INFO @ Sat, 03 Apr 2021 06:01:59: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (3034 records, 4 fields): 10 millis CompletedMACS2peakCalling