Job ID = 12264860 SRX = SRX3032259 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 8307451 spots for SRR5863949/SRR5863949.sra Written 8307451 spots for SRR5863949/SRR5863949.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265038 ("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: 00:03:23 8307451 reads; of these: 8307451 (100.00%) were unpaired; of these: 2676153 (32.21%) aligned 0 times 4877321 (58.71%) aligned exactly 1 time 753977 (9.08%) aligned >1 times 67.79% overall alignment rate Time searching: 00:03:23 Overall time: 00:03:23 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] 1615874 / 5631298 = 0.2869 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 05:59:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032259/SRX3032259.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032259/SRX3032259.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032259/SRX3032259.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032259/SRX3032259.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 05:59:59: #1 read tag files... INFO @ Sat, 03 Apr 2021 05:59:59: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:00:07: 1000000 INFO @ Sat, 03 Apr 2021 06:00:15: 2000000 INFO @ Sat, 03 Apr 2021 06:00:22: 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 06:00:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032259/SRX3032259.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032259/SRX3032259.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032259/SRX3032259.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032259/SRX3032259.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 06:00:29: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:00:29: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:00:30: 4000000 INFO @ Sat, 03 Apr 2021 06:00:30: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 06:00:30: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 06:00:30: #1 total tags in treatment: 4015424 INFO @ Sat, 03 Apr 2021 06:00:30: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:00:30: #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 06:00:30: #1 tags after filtering in treatment: 4015424 INFO @ Sat, 03 Apr 2021 06:00:30: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:00:30: #1 finished! INFO @ Sat, 03 Apr 2021 06:00:30: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:00:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:00:31: #2 number of paired peaks: 5303 INFO @ Sat, 03 Apr 2021 06:00:31: start model_add_line... INFO @ Sat, 03 Apr 2021 06:00:31: start X-correlation... INFO @ Sat, 03 Apr 2021 06:00:31: end of X-cor INFO @ Sat, 03 Apr 2021 06:00:31: #2 finished! INFO @ Sat, 03 Apr 2021 06:00:31: #2 predicted fragment length is 102 bps INFO @ Sat, 03 Apr 2021 06:00:31: #2 alternative fragment length(s) may be 102 bps INFO @ Sat, 03 Apr 2021 06:00:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032259/SRX3032259.05_model.r WARNING @ Sat, 03 Apr 2021 06:00:31: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:00:31: #2 You may need to consider one of the other alternative d(s): 102 WARNING @ Sat, 03 Apr 2021 06:00:31: #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 06:00:31: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:00:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:00:36: 1000000 INFO @ Sat, 03 Apr 2021 06:00:43: 2000000 INFO @ Sat, 03 Apr 2021 06:00:43: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:00:50: 3000000 INFO @ Sat, 03 Apr 2021 06:00:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032259/SRX3032259.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:00:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032259/SRX3032259.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:00:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032259/SRX3032259.05_summits.bed INFO @ Sat, 03 Apr 2021 06:00:51: Done! pass1 - making usageList (14 chroms): 6 millis pass2 - checking and writing primary data (13077 records, 4 fields): 21 millis CompletedMACS2peakCalling 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 06:00:57: 4000000 INFO @ Sat, 03 Apr 2021 06:00:57: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 06:00:57: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 06:00:57: #1 total tags in treatment: 4015424 INFO @ Sat, 03 Apr 2021 06:00:57: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:00:57: #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 06:00:57: #1 tags after filtering in treatment: 4015424 INFO @ Sat, 03 Apr 2021 06:00:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:00:57: #1 finished! INFO @ Sat, 03 Apr 2021 06:00:57: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:00:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:00:58: #2 number of paired peaks: 5303 INFO @ Sat, 03 Apr 2021 06:00:58: start model_add_line... INFO @ Sat, 03 Apr 2021 06:00:58: start X-correlation... INFO @ Sat, 03 Apr 2021 06:00:58: end of X-cor INFO @ Sat, 03 Apr 2021 06:00:58: #2 finished! INFO @ Sat, 03 Apr 2021 06:00:58: #2 predicted fragment length is 102 bps INFO @ Sat, 03 Apr 2021 06:00:58: #2 alternative fragment length(s) may be 102 bps INFO @ Sat, 03 Apr 2021 06:00:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032259/SRX3032259.10_model.r WARNING @ Sat, 03 Apr 2021 06:00:58: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:00:58: #2 You may need to consider one of the other alternative d(s): 102 WARNING @ Sat, 03 Apr 2021 06:00:58: #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 06:00:58: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:00:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:00:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032259/SRX3032259.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032259/SRX3032259.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032259/SRX3032259.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032259/SRX3032259.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 06:00:59: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:00:59: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:01:07: 1000000 INFO @ Sat, 03 Apr 2021 06:01:10: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:01:15: 2000000 INFO @ Sat, 03 Apr 2021 06:01:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032259/SRX3032259.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:01:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032259/SRX3032259.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:01:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032259/SRX3032259.10_summits.bed INFO @ Sat, 03 Apr 2021 06:01:17: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (7388 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:01:22: 3000000 INFO @ Sat, 03 Apr 2021 06:01:30: 4000000 INFO @ Sat, 03 Apr 2021 06:01:31: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 06:01:31: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 06:01:31: #1 total tags in treatment: 4015424 INFO @ Sat, 03 Apr 2021 06:01:31: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:01:31: #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 06:01:31: #1 tags after filtering in treatment: 4015424 INFO @ Sat, 03 Apr 2021 06:01:31: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:01:31: #1 finished! INFO @ Sat, 03 Apr 2021 06:01:31: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:01:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:01:31: #2 number of paired peaks: 5303 INFO @ Sat, 03 Apr 2021 06:01:31: start model_add_line... INFO @ Sat, 03 Apr 2021 06:01:31: start X-correlation... INFO @ Sat, 03 Apr 2021 06:01:31: end of X-cor INFO @ Sat, 03 Apr 2021 06:01:31: #2 finished! INFO @ Sat, 03 Apr 2021 06:01:31: #2 predicted fragment length is 102 bps INFO @ Sat, 03 Apr 2021 06:01:31: #2 alternative fragment length(s) may be 102 bps INFO @ Sat, 03 Apr 2021 06:01:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032259/SRX3032259.20_model.r WARNING @ Sat, 03 Apr 2021 06:01:31: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:01:31: #2 You may need to consider one of the other alternative d(s): 102 WARNING @ Sat, 03 Apr 2021 06:01:31: #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 06:01:31: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:01:31: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:01:44: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:01:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032259/SRX3032259.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:01:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032259/SRX3032259.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:01:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032259/SRX3032259.20_summits.bed INFO @ Sat, 03 Apr 2021 06:01:51: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (2655 records, 4 fields): 22 millis CompletedMACS2peakCalling