Job ID = 14170480 SRX = SRX8689041 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 17806125 spots for SRR12174241/SRR12174241.sra Written 17806125 spots for SRR12174241/SRR12174241.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170905 ("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: 00:06:21 17806125 reads; of these: 17806125 (100.00%) were unpaired; of these: 510824 (2.87%) aligned 0 times 11972652 (67.24%) aligned exactly 1 time 5322649 (29.89%) aligned >1 times 97.13% overall alignment rate Time searching: 00:06:21 Overall time: 00:06:21 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] 1478168 / 17295301 = 0.0855 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 07:05:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689041/SRX8689041.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689041/SRX8689041.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689041/SRX8689041.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689041/SRX8689041.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 07:05:30: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:05:30: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:05:36: 1000000 INFO @ Sat, 11 Dec 2021 07:05:42: 2000000 INFO @ Sat, 11 Dec 2021 07:05:47: 3000000 INFO @ Sat, 11 Dec 2021 07:05:52: 4000000 INFO @ Sat, 11 Dec 2021 07:05:58: 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 @ Sat, 11 Dec 2021 07:06:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689041/SRX8689041.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689041/SRX8689041.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689041/SRX8689041.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689041/SRX8689041.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 07:06:00: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:06:00: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:06:04: 6000000 INFO @ Sat, 11 Dec 2021 07:06:06: 1000000 INFO @ Sat, 11 Dec 2021 07:06:11: 7000000 INFO @ Sat, 11 Dec 2021 07:06:13: 2000000 INFO @ Sat, 11 Dec 2021 07:06:17: 8000000 INFO @ Sat, 11 Dec 2021 07:06:19: 3000000 INFO @ Sat, 11 Dec 2021 07:06:23: 9000000 INFO @ Sat, 11 Dec 2021 07:06:25: 4000000 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 @ Sat, 11 Dec 2021 07:06:30: 10000000 INFO @ Sat, 11 Dec 2021 07:06:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689041/SRX8689041.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689041/SRX8689041.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689041/SRX8689041.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689041/SRX8689041.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 07:06:30: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:06:30: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:06:32: 5000000 INFO @ Sat, 11 Dec 2021 07:06:37: 11000000 INFO @ Sat, 11 Dec 2021 07:06:38: 1000000 INFO @ Sat, 11 Dec 2021 07:06:38: 6000000 INFO @ Sat, 11 Dec 2021 07:06:44: 12000000 INFO @ Sat, 11 Dec 2021 07:06:45: 7000000 INFO @ Sat, 11 Dec 2021 07:06:45: 2000000 INFO @ Sat, 11 Dec 2021 07:06:51: 13000000 INFO @ Sat, 11 Dec 2021 07:06:51: 8000000 INFO @ Sat, 11 Dec 2021 07:06:52: 3000000 INFO @ Sat, 11 Dec 2021 07:06:58: 9000000 INFO @ Sat, 11 Dec 2021 07:06:58: 14000000 INFO @ Sat, 11 Dec 2021 07:07:00: 4000000 INFO @ Sat, 11 Dec 2021 07:07:04: 10000000 INFO @ Sat, 11 Dec 2021 07:07:04: 15000000 INFO @ Sat, 11 Dec 2021 07:07:07: 5000000 INFO @ Sat, 11 Dec 2021 07:07:10: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:07:10: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:07:10: #1 total tags in treatment: 15817133 INFO @ Sat, 11 Dec 2021 07:07:10: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:07:10: #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 07:07:10: #1 tags after filtering in treatment: 15817133 INFO @ Sat, 11 Dec 2021 07:07:10: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:07:10: #1 finished! INFO @ Sat, 11 Dec 2021 07:07:10: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:07:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:07:11: 11000000 INFO @ Sat, 11 Dec 2021 07:07:11: #2 number of paired peaks: 128 WARNING @ Sat, 11 Dec 2021 07:07:11: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Sat, 11 Dec 2021 07:07:11: start model_add_line... INFO @ Sat, 11 Dec 2021 07:07:11: start X-correlation... INFO @ Sat, 11 Dec 2021 07:07:11: end of X-cor INFO @ Sat, 11 Dec 2021 07:07:11: #2 finished! INFO @ Sat, 11 Dec 2021 07:07:11: #2 predicted fragment length is 47 bps INFO @ Sat, 11 Dec 2021 07:07:11: #2 alternative fragment length(s) may be 47 bps INFO @ Sat, 11 Dec 2021 07:07:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689041/SRX8689041.05_model.r WARNING @ Sat, 11 Dec 2021 07:07:11: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:07:11: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Sat, 11 Dec 2021 07:07:11: #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 07:07:11: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:07:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:07:14: 6000000 INFO @ Sat, 11 Dec 2021 07:07:17: 12000000 INFO @ Sat, 11 Dec 2021 07:07:22: 7000000 INFO @ Sat, 11 Dec 2021 07:07:24: 13000000 INFO @ Sat, 11 Dec 2021 07:07:29: 8000000 INFO @ Sat, 11 Dec 2021 07:07:30: 14000000 INFO @ Sat, 11 Dec 2021 07:07:36: 9000000 INFO @ Sat, 11 Dec 2021 07:07:37: 15000000 INFO @ Sat, 11 Dec 2021 07:07:39: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 07:07:42: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:07:42: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:07:42: #1 total tags in treatment: 15817133 INFO @ Sat, 11 Dec 2021 07:07:42: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:07:42: #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 07:07:43: #1 tags after filtering in treatment: 15817133 INFO @ Sat, 11 Dec 2021 07:07:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:07:43: #1 finished! INFO @ Sat, 11 Dec 2021 07:07:43: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:07:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:07:44: #2 number of paired peaks: 128 WARNING @ Sat, 11 Dec 2021 07:07:44: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Sat, 11 Dec 2021 07:07:44: start model_add_line... INFO @ Sat, 11 Dec 2021 07:07:44: start X-correlation... INFO @ Sat, 11 Dec 2021 07:07:44: end of X-cor INFO @ Sat, 11 Dec 2021 07:07:44: #2 finished! INFO @ Sat, 11 Dec 2021 07:07:44: #2 predicted fragment length is 47 bps INFO @ Sat, 11 Dec 2021 07:07:44: #2 alternative fragment length(s) may be 47 bps INFO @ Sat, 11 Dec 2021 07:07:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689041/SRX8689041.10_model.r WARNING @ Sat, 11 Dec 2021 07:07:44: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:07:44: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Sat, 11 Dec 2021 07:07:44: #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 07:07:44: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:07:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:07:44: 10000000 INFO @ Sat, 11 Dec 2021 07:07:50: 11000000 INFO @ Sat, 11 Dec 2021 07:07:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689041/SRX8689041.05_peaks.xls INFO @ Sat, 11 Dec 2021 07:07:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689041/SRX8689041.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:07:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689041/SRX8689041.05_summits.bed INFO @ Sat, 11 Dec 2021 07:07:54: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1867 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:07:57: 12000000 INFO @ Sat, 11 Dec 2021 07:08:04: 13000000 INFO @ Sat, 11 Dec 2021 07:08:11: 14000000 INFO @ Sat, 11 Dec 2021 07:08:13: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 07:08:17: 15000000 INFO @ Sat, 11 Dec 2021 07:08:23: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:08:23: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:08:23: #1 total tags in treatment: 15817133 INFO @ Sat, 11 Dec 2021 07:08:23: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:08:23: #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 07:08:23: #1 tags after filtering in treatment: 15817133 INFO @ Sat, 11 Dec 2021 07:08:23: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:08:23: #1 finished! INFO @ Sat, 11 Dec 2021 07:08:23: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:08:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:08:24: #2 number of paired peaks: 128 WARNING @ Sat, 11 Dec 2021 07:08:24: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Sat, 11 Dec 2021 07:08:24: start model_add_line... INFO @ Sat, 11 Dec 2021 07:08:24: start X-correlation... INFO @ Sat, 11 Dec 2021 07:08:24: end of X-cor INFO @ Sat, 11 Dec 2021 07:08:24: #2 finished! INFO @ Sat, 11 Dec 2021 07:08:24: #2 predicted fragment length is 47 bps INFO @ Sat, 11 Dec 2021 07:08:24: #2 alternative fragment length(s) may be 47 bps INFO @ Sat, 11 Dec 2021 07:08:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689041/SRX8689041.20_model.r WARNING @ Sat, 11 Dec 2021 07:08:24: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:08:24: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Sat, 11 Dec 2021 07:08:24: #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 07:08:24: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:08:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:08:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689041/SRX8689041.10_peaks.xls INFO @ Sat, 11 Dec 2021 07:08:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689041/SRX8689041.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:08:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689041/SRX8689041.10_summits.bed INFO @ Sat, 11 Dec 2021 07:08:28: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1376 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:08:53: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:09:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689041/SRX8689041.20_peaks.xls INFO @ Sat, 11 Dec 2021 07:09:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689041/SRX8689041.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:09:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689041/SRX8689041.20_summits.bed INFO @ Sat, 11 Dec 2021 07:09:07: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (1018 records, 4 fields): 2 millis CompletedMACS2peakCalling