Job ID = 12265396 SRX = SRX7191479 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 21282276 spots for SRR10502463/SRR10502463.sra Written 21282276 spots for SRR10502463/SRR10502463.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265518 ("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: 00:05:28 21282276 reads; of these: 21282276 (100.00%) were unpaired; of these: 3930782 (18.47%) aligned 0 times 12130072 (57.00%) aligned exactly 1 time 5221422 (24.53%) aligned >1 times 81.53% overall alignment rate Time searching: 00:05:28 Overall time: 00:05:28 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 8 files... [bam_rmdupse_core] 6006230 / 17351494 = 0.3462 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 06:59:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7191479/SRX7191479.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7191479/SRX7191479.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7191479/SRX7191479.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7191479/SRX7191479.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 06:59:25: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:59:25: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:59:30: 1000000 INFO @ Sat, 03 Apr 2021 06:59:36: 2000000 INFO @ Sat, 03 Apr 2021 06:59:41: 3000000 INFO @ Sat, 03 Apr 2021 06:59:47: 4000000 INFO @ Sat, 03 Apr 2021 06:59:52: 5000000 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 06:59:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7191479/SRX7191479.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7191479/SRX7191479.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7191479/SRX7191479.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7191479/SRX7191479.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 06:59:55: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:59:55: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:59:58: 6000000 INFO @ Sat, 03 Apr 2021 07:00:01: 1000000 INFO @ Sat, 03 Apr 2021 07:00:03: 7000000 INFO @ Sat, 03 Apr 2021 07:00:07: 2000000 INFO @ Sat, 03 Apr 2021 07:00:09: 8000000 INFO @ Sat, 03 Apr 2021 07:00:13: 3000000 INFO @ Sat, 03 Apr 2021 07:00:14: 9000000 INFO @ Sat, 03 Apr 2021 07:00:20: 4000000 INFO @ Sat, 03 Apr 2021 07:00:20: 10000000 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 07:00:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7191479/SRX7191479.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7191479/SRX7191479.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7191479/SRX7191479.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7191479/SRX7191479.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 07:00:24: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:00:24: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:00:25: 11000000 INFO @ Sat, 03 Apr 2021 07:00:26: 5000000 INFO @ Sat, 03 Apr 2021 07:00:27: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:00:27: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:00:27: #1 total tags in treatment: 11345264 INFO @ Sat, 03 Apr 2021 07:00:27: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:00:27: #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 07:00:28: #1 tags after filtering in treatment: 11345264 INFO @ Sat, 03 Apr 2021 07:00:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 07:00:28: #1 finished! INFO @ Sat, 03 Apr 2021 07:00:28: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:00:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:00:28: #2 number of paired peaks: 194 WARNING @ Sat, 03 Apr 2021 07:00:28: Fewer paired peaks (194) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 194 pairs to build model! INFO @ Sat, 03 Apr 2021 07:00:28: start model_add_line... INFO @ Sat, 03 Apr 2021 07:00:29: start X-correlation... INFO @ Sat, 03 Apr 2021 07:00:29: end of X-cor INFO @ Sat, 03 Apr 2021 07:00:29: #2 finished! INFO @ Sat, 03 Apr 2021 07:00:29: #2 predicted fragment length is 46 bps INFO @ Sat, 03 Apr 2021 07:00:29: #2 alternative fragment length(s) may be 4,46 bps INFO @ Sat, 03 Apr 2021 07:00:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7191479/SRX7191479.05_model.r WARNING @ Sat, 03 Apr 2021 07:00:29: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:00:29: #2 You may need to consider one of the other alternative d(s): 4,46 WARNING @ Sat, 03 Apr 2021 07:00:29: #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 07:00:29: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:00:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:00:30: 1000000 INFO @ Sat, 03 Apr 2021 07:00:32: 6000000 INFO @ Sat, 03 Apr 2021 07:00:36: 2000000 INFO @ Sat, 03 Apr 2021 07:00:39: 7000000 INFO @ Sat, 03 Apr 2021 07:00:41: 3000000 INFO @ Sat, 03 Apr 2021 07:00:45: 8000000 INFO @ Sat, 03 Apr 2021 07:00:47: 4000000 INFO @ Sat, 03 Apr 2021 07:00:51: 9000000 INFO @ Sat, 03 Apr 2021 07:00:52: 5000000 INFO @ Sat, 03 Apr 2021 07:00:56: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:00:57: 10000000 INFO @ Sat, 03 Apr 2021 07:00:58: 6000000 INFO @ Sat, 03 Apr 2021 07:01:03: 11000000 INFO @ Sat, 03 Apr 2021 07:01:03: 7000000 INFO @ Sat, 03 Apr 2021 07:01:05: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:01:05: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:01:05: #1 total tags in treatment: 11345264 INFO @ Sat, 03 Apr 2021 07:01:05: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:01:05: #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 07:01:05: #1 tags after filtering in treatment: 11345264 INFO @ Sat, 03 Apr 2021 07:01:05: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 07:01:05: #1 finished! INFO @ Sat, 03 Apr 2021 07:01:05: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:01:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:01:06: #2 number of paired peaks: 194 WARNING @ Sat, 03 Apr 2021 07:01:06: Fewer paired peaks (194) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 194 pairs to build model! INFO @ Sat, 03 Apr 2021 07:01:06: start model_add_line... INFO @ Sat, 03 Apr 2021 07:01:06: start X-correlation... INFO @ Sat, 03 Apr 2021 07:01:06: end of X-cor INFO @ Sat, 03 Apr 2021 07:01:06: #2 finished! INFO @ Sat, 03 Apr 2021 07:01:06: #2 predicted fragment length is 46 bps INFO @ Sat, 03 Apr 2021 07:01:06: #2 alternative fragment length(s) may be 4,46 bps INFO @ Sat, 03 Apr 2021 07:01:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7191479/SRX7191479.10_model.r WARNING @ Sat, 03 Apr 2021 07:01:06: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:01:06: #2 You may need to consider one of the other alternative d(s): 4,46 WARNING @ Sat, 03 Apr 2021 07:01:06: #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 07:01:06: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:01:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:01:09: 8000000 INFO @ Sat, 03 Apr 2021 07:01:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7191479/SRX7191479.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:01:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7191479/SRX7191479.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:01:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7191479/SRX7191479.05_summits.bed INFO @ Sat, 03 Apr 2021 07:01:10: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5148 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:01:14: 9000000 INFO @ Sat, 03 Apr 2021 07:01:19: 10000000 INFO @ Sat, 03 Apr 2021 07:01:24: 11000000 INFO @ Sat, 03 Apr 2021 07:01:26: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:01:26: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:01:26: #1 total tags in treatment: 11345264 INFO @ Sat, 03 Apr 2021 07:01:26: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:01:26: #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 07:01:26: #1 tags after filtering in treatment: 11345264 INFO @ Sat, 03 Apr 2021 07:01:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 07:01:26: #1 finished! INFO @ Sat, 03 Apr 2021 07:01:26: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:01:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:01:27: #2 number of paired peaks: 194 WARNING @ Sat, 03 Apr 2021 07:01:27: Fewer paired peaks (194) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 194 pairs to build model! INFO @ Sat, 03 Apr 2021 07:01:27: start model_add_line... INFO @ Sat, 03 Apr 2021 07:01:27: start X-correlation... INFO @ Sat, 03 Apr 2021 07:01:27: end of X-cor INFO @ Sat, 03 Apr 2021 07:01:27: #2 finished! INFO @ Sat, 03 Apr 2021 07:01:27: #2 predicted fragment length is 46 bps INFO @ Sat, 03 Apr 2021 07:01:27: #2 alternative fragment length(s) may be 4,46 bps INFO @ Sat, 03 Apr 2021 07:01:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7191479/SRX7191479.20_model.r WARNING @ Sat, 03 Apr 2021 07:01:27: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:01:27: #2 You may need to consider one of the other alternative d(s): 4,46 WARNING @ Sat, 03 Apr 2021 07:01:27: #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 07:01:27: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:01:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:01:31: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:01:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7191479/SRX7191479.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:01:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7191479/SRX7191479.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:01:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7191479/SRX7191479.10_summits.bed INFO @ Sat, 03 Apr 2021 07:01:45: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1041 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:01:53: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:02:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7191479/SRX7191479.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:02:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7191479/SRX7191479.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:02:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7191479/SRX7191479.20_summits.bed INFO @ Sat, 03 Apr 2021 07:02:07: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (17 records, 4 fields): 1 millis CompletedMACS2peakCalling