Job ID = 16438044 SRX = SRX12261348 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 17572642 spots for SRR15972604/SRR15972604.sra Written 17572642 spots for SRR15972604/SRR15972604.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438111 ("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: 00:10:35 17572642 reads; of these: 17572642 (100.00%) were unpaired; of these: 1226856 (6.98%) aligned 0 times 10198394 (58.04%) aligned exactly 1 time 6147392 (34.98%) aligned >1 times 93.02% overall alignment rate Time searching: 00:10:35 Overall time: 00:10:35 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] 11140750 / 16345786 = 0.6816 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 13:37:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12261348/SRX12261348.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12261348/SRX12261348.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12261348/SRX12261348.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12261348/SRX12261348.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 @ Tue, 02 Aug 2022 13:37:29: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:37:29: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:37:34: 1000000 INFO @ Tue, 02 Aug 2022 13:37:40: 2000000 INFO @ Tue, 02 Aug 2022 13:37:45: 3000000 INFO @ Tue, 02 Aug 2022 13:37:50: 4000000 INFO @ Tue, 02 Aug 2022 13:37:56: 5000000 INFO @ Tue, 02 Aug 2022 13:37:57: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:37:57: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:37:57: #1 total tags in treatment: 5205036 INFO @ Tue, 02 Aug 2022 13:37:57: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:37:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 13:37:57: #1 tags after filtering in treatment: 5205036 INFO @ Tue, 02 Aug 2022 13:37:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:37:57: #1 finished! INFO @ Tue, 02 Aug 2022 13:37:57: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:37:57: #2 looking for paired plus/minus strand peaks... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 13:37:57: #2 number of paired peaks: 1761 INFO @ Tue, 02 Aug 2022 13:37:57: start model_add_line... INFO @ Tue, 02 Aug 2022 13:37:57: start X-correlation... INFO @ Tue, 02 Aug 2022 13:37:58: end of X-cor INFO @ Tue, 02 Aug 2022 13:37:58: #2 finished! INFO @ Tue, 02 Aug 2022 13:37:58: #2 predicted fragment length is 76 bps INFO @ Tue, 02 Aug 2022 13:37:58: #2 alternative fragment length(s) may be 76 bps INFO @ Tue, 02 Aug 2022 13:37:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12261348/SRX12261348.05_model.r WARNING @ Tue, 02 Aug 2022 13:37:58: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:37:58: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Tue, 02 Aug 2022 13:37:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 13:37:58: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:37:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:37:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12261348/SRX12261348.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12261348/SRX12261348.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12261348/SRX12261348.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12261348/SRX12261348.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 @ Tue, 02 Aug 2022 13:37:59: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:37:59: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:38:05: 1000000 INFO @ Tue, 02 Aug 2022 13:38:08: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:38:12: 2000000 INFO @ Tue, 02 Aug 2022 13:38:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12261348/SRX12261348.05_peaks.xls INFO @ Tue, 02 Aug 2022 13:38:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12261348/SRX12261348.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:38:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12261348/SRX12261348.05_summits.bed INFO @ Tue, 02 Aug 2022 13:38:14: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6732 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:38:18: 3000000 INFO @ Tue, 02 Aug 2022 13:38:24: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 13:38:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12261348/SRX12261348.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12261348/SRX12261348.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12261348/SRX12261348.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12261348/SRX12261348.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 @ Tue, 02 Aug 2022 13:38:29: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:38:29: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:38:31: 5000000 INFO @ Tue, 02 Aug 2022 13:38:32: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:38:32: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:38:32: #1 total tags in treatment: 5205036 INFO @ Tue, 02 Aug 2022 13:38:32: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:38:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 13:38:32: #1 tags after filtering in treatment: 5205036 INFO @ Tue, 02 Aug 2022 13:38:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:38:32: #1 finished! INFO @ Tue, 02 Aug 2022 13:38:32: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:38:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:38:33: #2 number of paired peaks: 1761 INFO @ Tue, 02 Aug 2022 13:38:33: start model_add_line... INFO @ Tue, 02 Aug 2022 13:38:33: start X-correlation... INFO @ Tue, 02 Aug 2022 13:38:33: end of X-cor INFO @ Tue, 02 Aug 2022 13:38:33: #2 finished! INFO @ Tue, 02 Aug 2022 13:38:33: #2 predicted fragment length is 76 bps INFO @ Tue, 02 Aug 2022 13:38:33: #2 alternative fragment length(s) may be 76 bps INFO @ Tue, 02 Aug 2022 13:38:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12261348/SRX12261348.10_model.r WARNING @ Tue, 02 Aug 2022 13:38:33: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:38:33: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Tue, 02 Aug 2022 13:38:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 13:38:33: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:38:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:38:35: 1000000 INFO @ Tue, 02 Aug 2022 13:38:41: 2000000 INFO @ Tue, 02 Aug 2022 13:38:44: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:38:47: 3000000 INFO @ Tue, 02 Aug 2022 13:38:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12261348/SRX12261348.10_peaks.xls INFO @ Tue, 02 Aug 2022 13:38:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12261348/SRX12261348.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:38:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12261348/SRX12261348.10_summits.bed INFO @ Tue, 02 Aug 2022 13:38:50: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2884 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:38:52: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 13:38:58: 5000000 INFO @ Tue, 02 Aug 2022 13:38:59: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:38:59: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:38:59: #1 total tags in treatment: 5205036 INFO @ Tue, 02 Aug 2022 13:38:59: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:38:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 13:38:59: #1 tags after filtering in treatment: 5205036 INFO @ Tue, 02 Aug 2022 13:38:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:38:59: #1 finished! INFO @ Tue, 02 Aug 2022 13:38:59: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:38:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:39:00: #2 number of paired peaks: 1761 INFO @ Tue, 02 Aug 2022 13:39:00: start model_add_line... INFO @ Tue, 02 Aug 2022 13:39:00: start X-correlation... INFO @ Tue, 02 Aug 2022 13:39:00: end of X-cor INFO @ Tue, 02 Aug 2022 13:39:00: #2 finished! INFO @ Tue, 02 Aug 2022 13:39:00: #2 predicted fragment length is 76 bps INFO @ Tue, 02 Aug 2022 13:39:00: #2 alternative fragment length(s) may be 76 bps INFO @ Tue, 02 Aug 2022 13:39:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12261348/SRX12261348.20_model.r WARNING @ Tue, 02 Aug 2022 13:39:00: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:39:00: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Tue, 02 Aug 2022 13:39:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 13:39:00: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:39:00: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 13:39:11: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:39:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12261348/SRX12261348.20_peaks.xls INFO @ Tue, 02 Aug 2022 13:39:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12261348/SRX12261348.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:39:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12261348/SRX12261348.20_summits.bed INFO @ Tue, 02 Aug 2022 13:39:16: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (801 records, 4 fields): 28 millis CompletedMACS2peakCalling