Job ID = 14167026 SRX = SRX8574261 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 28057317 spots for SRR12045582/SRR12045582.sra Written 28057317 spots for SRR12045582/SRR12045582.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167384 ("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: 00:08:24 28057317 reads; of these: 28057317 (100.00%) were unpaired; of these: 8073725 (28.78%) aligned 0 times 12954004 (46.17%) aligned exactly 1 time 7029588 (25.05%) aligned >1 times 71.22% overall alignment rate Time searching: 00:08:24 Overall time: 00:08:24 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 12 files... [bam_rmdupse_core] 4981084 / 19983592 = 0.2493 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 @ Fri, 10 Dec 2021 09:06:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8574261/SRX8574261.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8574261/SRX8574261.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8574261/SRX8574261.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8574261/SRX8574261.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 @ Fri, 10 Dec 2021 09:06:37: #1 read tag files... INFO @ Fri, 10 Dec 2021 09:06:37: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 09:06:43: 1000000 INFO @ Fri, 10 Dec 2021 09:06:48: 2000000 INFO @ Fri, 10 Dec 2021 09:06:54: 3000000 INFO @ Fri, 10 Dec 2021 09:06:59: 4000000 INFO @ Fri, 10 Dec 2021 09:07:05: 5000000 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 @ Fri, 10 Dec 2021 09:07:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8574261/SRX8574261.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8574261/SRX8574261.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8574261/SRX8574261.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8574261/SRX8574261.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 @ Fri, 10 Dec 2021 09:07:07: #1 read tag files... INFO @ Fri, 10 Dec 2021 09:07:07: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 09:07:11: 6000000 INFO @ Fri, 10 Dec 2021 09:07:13: 1000000 INFO @ Fri, 10 Dec 2021 09:07:16: 7000000 INFO @ Fri, 10 Dec 2021 09:07:18: 2000000 INFO @ Fri, 10 Dec 2021 09:07:22: 8000000 INFO @ Fri, 10 Dec 2021 09:07:23: 3000000 INFO @ Fri, 10 Dec 2021 09:07:28: 9000000 INFO @ Fri, 10 Dec 2021 09:07:28: 4000000 INFO @ Fri, 10 Dec 2021 09:07:33: 5000000 INFO @ Fri, 10 Dec 2021 09:07:33: 10000000 BedGraph に変換中... 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 @ Fri, 10 Dec 2021 09:07:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8574261/SRX8574261.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8574261/SRX8574261.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8574261/SRX8574261.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8574261/SRX8574261.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 @ Fri, 10 Dec 2021 09:07:37: #1 read tag files... INFO @ Fri, 10 Dec 2021 09:07:37: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 09:07:38: 6000000 INFO @ Fri, 10 Dec 2021 09:07:39: 11000000 INFO @ Fri, 10 Dec 2021 09:07:43: 7000000 INFO @ Fri, 10 Dec 2021 09:07:44: 1000000 INFO @ Fri, 10 Dec 2021 09:07:45: 12000000 INFO @ Fri, 10 Dec 2021 09:07:48: 8000000 INFO @ Fri, 10 Dec 2021 09:07:49: 2000000 INFO @ Fri, 10 Dec 2021 09:07:50: 13000000 INFO @ Fri, 10 Dec 2021 09:07:53: 9000000 INFO @ Fri, 10 Dec 2021 09:07:55: 3000000 INFO @ Fri, 10 Dec 2021 09:07:56: 14000000 INFO @ Fri, 10 Dec 2021 09:07:59: 10000000 INFO @ Fri, 10 Dec 2021 09:08:01: 4000000 INFO @ Fri, 10 Dec 2021 09:08:02: 15000000 INFO @ Fri, 10 Dec 2021 09:08:02: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 09:08:02: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 09:08:02: #1 total tags in treatment: 15002508 INFO @ Fri, 10 Dec 2021 09:08:02: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 09:08:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 09:08:02: #1 tags after filtering in treatment: 15002508 INFO @ Fri, 10 Dec 2021 09:08:02: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 09:08:02: #1 finished! INFO @ Fri, 10 Dec 2021 09:08:02: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 09:08:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 09:08:03: #2 number of paired peaks: 115 WARNING @ Fri, 10 Dec 2021 09:08:03: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Fri, 10 Dec 2021 09:08:03: start model_add_line... INFO @ Fri, 10 Dec 2021 09:08:03: start X-correlation... INFO @ Fri, 10 Dec 2021 09:08:03: end of X-cor INFO @ Fri, 10 Dec 2021 09:08:03: #2 finished! INFO @ Fri, 10 Dec 2021 09:08:03: #2 predicted fragment length is 56 bps INFO @ Fri, 10 Dec 2021 09:08:03: #2 alternative fragment length(s) may be 4,56 bps INFO @ Fri, 10 Dec 2021 09:08:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8574261/SRX8574261.05_model.r WARNING @ Fri, 10 Dec 2021 09:08:03: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 09:08:03: #2 You may need to consider one of the other alternative d(s): 4,56 WARNING @ Fri, 10 Dec 2021 09:08:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 09:08:03: #3 Call peaks... INFO @ Fri, 10 Dec 2021 09:08:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 09:08:04: 11000000 INFO @ Fri, 10 Dec 2021 09:08:07: 5000000 INFO @ Fri, 10 Dec 2021 09:08:09: 12000000 INFO @ Fri, 10 Dec 2021 09:08:13: 6000000 INFO @ Fri, 10 Dec 2021 09:08:14: 13000000 INFO @ Fri, 10 Dec 2021 09:08:18: 7000000 INFO @ Fri, 10 Dec 2021 09:08:19: 14000000 INFO @ Fri, 10 Dec 2021 09:08:24: 15000000 INFO @ Fri, 10 Dec 2021 09:08:24: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 09:08:24: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 09:08:24: #1 total tags in treatment: 15002508 INFO @ Fri, 10 Dec 2021 09:08:24: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 09:08:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 09:08:24: 8000000 INFO @ Fri, 10 Dec 2021 09:08:24: #1 tags after filtering in treatment: 15002508 INFO @ Fri, 10 Dec 2021 09:08:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 09:08:24: #1 finished! INFO @ Fri, 10 Dec 2021 09:08:24: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 09:08:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 09:08:25: #2 number of paired peaks: 115 WARNING @ Fri, 10 Dec 2021 09:08:25: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Fri, 10 Dec 2021 09:08:25: start model_add_line... INFO @ Fri, 10 Dec 2021 09:08:25: start X-correlation... INFO @ Fri, 10 Dec 2021 09:08:25: end of X-cor INFO @ Fri, 10 Dec 2021 09:08:25: #2 finished! INFO @ Fri, 10 Dec 2021 09:08:25: #2 predicted fragment length is 56 bps INFO @ Fri, 10 Dec 2021 09:08:25: #2 alternative fragment length(s) may be 4,56 bps INFO @ Fri, 10 Dec 2021 09:08:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8574261/SRX8574261.10_model.r WARNING @ Fri, 10 Dec 2021 09:08:25: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 09:08:25: #2 You may need to consider one of the other alternative d(s): 4,56 WARNING @ Fri, 10 Dec 2021 09:08:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 09:08:25: #3 Call peaks... INFO @ Fri, 10 Dec 2021 09:08:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 09:08:30: 9000000 INFO @ Fri, 10 Dec 2021 09:08:32: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 09:08:35: 10000000 INFO @ Fri, 10 Dec 2021 09:08:41: 11000000 INFO @ Fri, 10 Dec 2021 09:08:47: 12000000 INFO @ Fri, 10 Dec 2021 09:08:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8574261/SRX8574261.05_peaks.xls INFO @ Fri, 10 Dec 2021 09:08:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8574261/SRX8574261.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 09:08:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8574261/SRX8574261.05_summits.bed INFO @ Fri, 10 Dec 2021 09:08:48: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1674 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 09:08:52: 13000000 INFO @ Fri, 10 Dec 2021 09:08:55: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 09:08:58: 14000000 INFO @ Fri, 10 Dec 2021 09:09:04: 15000000 INFO @ Fri, 10 Dec 2021 09:09:04: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 09:09:04: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 09:09:04: #1 total tags in treatment: 15002508 INFO @ Fri, 10 Dec 2021 09:09:04: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 09:09:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 09:09:04: #1 tags after filtering in treatment: 15002508 INFO @ Fri, 10 Dec 2021 09:09:04: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 09:09:04: #1 finished! INFO @ Fri, 10 Dec 2021 09:09:04: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 09:09:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 09:09:05: #2 number of paired peaks: 115 WARNING @ Fri, 10 Dec 2021 09:09:05: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Fri, 10 Dec 2021 09:09:05: start model_add_line... INFO @ Fri, 10 Dec 2021 09:09:05: start X-correlation... INFO @ Fri, 10 Dec 2021 09:09:05: end of X-cor INFO @ Fri, 10 Dec 2021 09:09:05: #2 finished! INFO @ Fri, 10 Dec 2021 09:09:05: #2 predicted fragment length is 56 bps INFO @ Fri, 10 Dec 2021 09:09:05: #2 alternative fragment length(s) may be 4,56 bps INFO @ Fri, 10 Dec 2021 09:09:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8574261/SRX8574261.20_model.r WARNING @ Fri, 10 Dec 2021 09:09:05: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 09:09:05: #2 You may need to consider one of the other alternative d(s): 4,56 WARNING @ Fri, 10 Dec 2021 09:09:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 09:09:05: #3 Call peaks... INFO @ Fri, 10 Dec 2021 09:09:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 09:09:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8574261/SRX8574261.10_peaks.xls INFO @ Fri, 10 Dec 2021 09:09:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8574261/SRX8574261.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 09:09:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8574261/SRX8574261.10_summits.bed INFO @ Fri, 10 Dec 2021 09:09:09: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1202 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 09:09:36: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 09:09:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8574261/SRX8574261.20_peaks.xls INFO @ Fri, 10 Dec 2021 09:09:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8574261/SRX8574261.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 09:09:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8574261/SRX8574261.20_summits.bed INFO @ Fri, 10 Dec 2021 09:09:50: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (737 records, 4 fields): 2 millis CompletedMACS2peakCalling