Job ID = 14170489 SRX = SRX8689050 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 6098509 spots for SRR12174193/SRR12174193.sra Written 6098509 spots for SRR12174193/SRR12174193.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170892 ("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: 00:02:09 6098509 reads; of these: 6098509 (100.00%) were unpaired; of these: 831560 (13.64%) aligned 0 times 4131410 (67.74%) aligned exactly 1 time 1135539 (18.62%) aligned >1 times 86.36% overall alignment rate Time searching: 00:02:10 Overall time: 00:02:10 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] 181242 / 5266949 = 0.0344 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 @ Sat, 11 Dec 2021 07:00:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689050/SRX8689050.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689050/SRX8689050.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689050/SRX8689050.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689050/SRX8689050.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, 11 Dec 2021 07:00:48: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:00:48: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:00:54: 1000000 INFO @ Sat, 11 Dec 2021 07:00:59: 2000000 INFO @ Sat, 11 Dec 2021 07:01:04: 3000000 INFO @ Sat, 11 Dec 2021 07:01:09: 4000000 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 @ Sat, 11 Dec 2021 07:01:15: 5000000 INFO @ Sat, 11 Dec 2021 07:01:15: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:01:15: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:01:15: #1 total tags in treatment: 5085707 INFO @ Sat, 11 Dec 2021 07:01:15: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:01:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 07:01:15: #1 tags after filtering in treatment: 5085707 INFO @ Sat, 11 Dec 2021 07:01:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:01:15: #1 finished! INFO @ Sat, 11 Dec 2021 07:01:15: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:01:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:01:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689050/SRX8689050.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689050/SRX8689050.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689050/SRX8689050.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689050/SRX8689050.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, 11 Dec 2021 07:01:16: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:01:16: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:01:16: #2 number of paired peaks: 354 WARNING @ Sat, 11 Dec 2021 07:01:16: Fewer paired peaks (354) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 354 pairs to build model! INFO @ Sat, 11 Dec 2021 07:01:16: start model_add_line... INFO @ Sat, 11 Dec 2021 07:01:16: start X-correlation... INFO @ Sat, 11 Dec 2021 07:01:16: end of X-cor INFO @ Sat, 11 Dec 2021 07:01:16: #2 finished! INFO @ Sat, 11 Dec 2021 07:01:16: #2 predicted fragment length is 49 bps INFO @ Sat, 11 Dec 2021 07:01:16: #2 alternative fragment length(s) may be 49 bps INFO @ Sat, 11 Dec 2021 07:01:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689050/SRX8689050.05_model.r WARNING @ Sat, 11 Dec 2021 07:01:16: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:01:16: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Sat, 11 Dec 2021 07:01:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 07:01:16: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:01:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:01:21: 1000000 INFO @ Sat, 11 Dec 2021 07:01:25: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:01:27: 2000000 INFO @ Sat, 11 Dec 2021 07:01:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689050/SRX8689050.05_peaks.xls INFO @ Sat, 11 Dec 2021 07:01:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689050/SRX8689050.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:01:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689050/SRX8689050.05_summits.bed INFO @ Sat, 11 Dec 2021 07:01:31: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1239 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:01:32: 3000000 INFO @ Sat, 11 Dec 2021 07:01:37: 4000000 INFO @ Sat, 11 Dec 2021 07:01:42: 5000000 INFO @ Sat, 11 Dec 2021 07:01:43: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:01:43: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:01:43: #1 total tags in treatment: 5085707 INFO @ Sat, 11 Dec 2021 07:01:43: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:01:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換中... INFO @ Sat, 11 Dec 2021 07:01:43: #1 tags after filtering in treatment: 5085707 INFO @ Sat, 11 Dec 2021 07:01:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:01:43: #1 finished! INFO @ Sat, 11 Dec 2021 07:01:43: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:01:43: #2 looking for paired plus/minus strand peaks... 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 @ Sat, 11 Dec 2021 07:01:43: #2 number of paired peaks: 354 WARNING @ Sat, 11 Dec 2021 07:01:43: Fewer paired peaks (354) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 354 pairs to build model! INFO @ Sat, 11 Dec 2021 07:01:43: start model_add_line... INFO @ Sat, 11 Dec 2021 07:01:43: start X-correlation... INFO @ Sat, 11 Dec 2021 07:01:43: end of X-cor INFO @ Sat, 11 Dec 2021 07:01:43: #2 finished! INFO @ Sat, 11 Dec 2021 07:01:43: #2 predicted fragment length is 49 bps INFO @ Sat, 11 Dec 2021 07:01:43: #2 alternative fragment length(s) may be 49 bps INFO @ Sat, 11 Dec 2021 07:01:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689050/SRX8689050.10_model.r WARNING @ Sat, 11 Dec 2021 07:01:44: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:01:44: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Sat, 11 Dec 2021 07:01:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 07:01:44: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:01:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:01:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689050/SRX8689050.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689050/SRX8689050.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689050/SRX8689050.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689050/SRX8689050.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, 11 Dec 2021 07:01:46: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:01:46: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:01:51: 1000000 INFO @ Sat, 11 Dec 2021 07:01:54: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:01:57: 2000000 INFO @ Sat, 11 Dec 2021 07:01:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689050/SRX8689050.10_peaks.xls INFO @ Sat, 11 Dec 2021 07:01:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689050/SRX8689050.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:01:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689050/SRX8689050.10_summits.bed INFO @ Sat, 11 Dec 2021 07:01:59: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (1029 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:02:02: 3000000 INFO @ Sat, 11 Dec 2021 07:02:07: 4000000 INFO @ Sat, 11 Dec 2021 07:02:13: 5000000 INFO @ Sat, 11 Dec 2021 07:02:13: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:02:13: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:02:13: #1 total tags in treatment: 5085707 INFO @ Sat, 11 Dec 2021 07:02:13: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:02:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 07:02:13: #1 tags after filtering in treatment: 5085707 INFO @ Sat, 11 Dec 2021 07:02:13: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:02:13: #1 finished! INFO @ Sat, 11 Dec 2021 07:02:13: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:02:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:02:14: #2 number of paired peaks: 354 WARNING @ Sat, 11 Dec 2021 07:02:14: Fewer paired peaks (354) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 354 pairs to build model! INFO @ Sat, 11 Dec 2021 07:02:14: start model_add_line... INFO @ Sat, 11 Dec 2021 07:02:14: start X-correlation... INFO @ Sat, 11 Dec 2021 07:02:14: end of X-cor INFO @ Sat, 11 Dec 2021 07:02:14: #2 finished! INFO @ Sat, 11 Dec 2021 07:02:14: #2 predicted fragment length is 49 bps INFO @ Sat, 11 Dec 2021 07:02:14: #2 alternative fragment length(s) may be 49 bps INFO @ Sat, 11 Dec 2021 07:02:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689050/SRX8689050.20_model.r WARNING @ Sat, 11 Dec 2021 07:02:14: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:02:14: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Sat, 11 Dec 2021 07:02:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 07:02:14: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:02:14: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 07:02:23: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:02:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689050/SRX8689050.20_peaks.xls INFO @ Sat, 11 Dec 2021 07:02:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689050/SRX8689050.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:02:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689050/SRX8689050.20_summits.bed INFO @ Sat, 11 Dec 2021 07:02:30: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (659 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。