Job ID = 14170368 SRX = SRX9720903 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 29367008 spots for SRR13291893/SRR13291893.sra Written 29367008 spots for SRR13291893/SRR13291893.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170771 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:09:51 29367008 reads; of these: 29367008 (100.00%) were unpaired; of these: 1089082 (3.71%) aligned 0 times 19540274 (66.54%) aligned exactly 1 time 8737652 (29.75%) aligned >1 times 96.29% overall alignment rate Time searching: 00:09:52 Overall time: 00:09:52 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] 6133817 / 28277926 = 0.2169 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 06:38:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720903/SRX9720903.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720903/SRX9720903.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720903/SRX9720903.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720903/SRX9720903.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 06:38:52: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:38:52: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:38:58: 1000000 INFO @ Sat, 11 Dec 2021 06:39:03: 2000000 INFO @ Sat, 11 Dec 2021 06:39:08: 3000000 INFO @ Sat, 11 Dec 2021 06:39:14: 4000000 INFO @ Sat, 11 Dec 2021 06:39:19: 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 06:39:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720903/SRX9720903.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720903/SRX9720903.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720903/SRX9720903.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720903/SRX9720903.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 06:39:22: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:39:22: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:39:24: 6000000 INFO @ Sat, 11 Dec 2021 06:39:28: 1000000 INFO @ Sat, 11 Dec 2021 06:39:30: 7000000 INFO @ Sat, 11 Dec 2021 06:39:33: 2000000 INFO @ Sat, 11 Dec 2021 06:39:35: 8000000 INFO @ Sat, 11 Dec 2021 06:39:39: 3000000 INFO @ Sat, 11 Dec 2021 06:39:41: 9000000 INFO @ Sat, 11 Dec 2021 06:39:45: 4000000 INFO @ Sat, 11 Dec 2021 06:39:47: 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 @ Sat, 11 Dec 2021 06:39:50: 5000000 INFO @ Sat, 11 Dec 2021 06:39:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720903/SRX9720903.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720903/SRX9720903.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720903/SRX9720903.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720903/SRX9720903.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 06:39:52: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:39:52: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:39:52: 11000000 INFO @ Sat, 11 Dec 2021 06:39:56: 6000000 INFO @ Sat, 11 Dec 2021 06:39:58: 1000000 INFO @ Sat, 11 Dec 2021 06:39:58: 12000000 INFO @ Sat, 11 Dec 2021 06:40:02: 7000000 INFO @ Sat, 11 Dec 2021 06:40:03: 2000000 INFO @ Sat, 11 Dec 2021 06:40:04: 13000000 INFO @ Sat, 11 Dec 2021 06:40:07: 8000000 INFO @ Sat, 11 Dec 2021 06:40:09: 3000000 INFO @ Sat, 11 Dec 2021 06:40:10: 14000000 INFO @ Sat, 11 Dec 2021 06:40:13: 9000000 INFO @ Sat, 11 Dec 2021 06:40:15: 4000000 INFO @ Sat, 11 Dec 2021 06:40:15: 15000000 INFO @ Sat, 11 Dec 2021 06:40:19: 10000000 INFO @ Sat, 11 Dec 2021 06:40:20: 5000000 INFO @ Sat, 11 Dec 2021 06:40:21: 16000000 INFO @ Sat, 11 Dec 2021 06:40:24: 11000000 INFO @ Sat, 11 Dec 2021 06:40:26: 6000000 INFO @ Sat, 11 Dec 2021 06:40:27: 17000000 INFO @ Sat, 11 Dec 2021 06:40:30: 12000000 INFO @ Sat, 11 Dec 2021 06:40:32: 7000000 INFO @ Sat, 11 Dec 2021 06:40:32: 18000000 INFO @ Sat, 11 Dec 2021 06:40:36: 13000000 INFO @ Sat, 11 Dec 2021 06:40:37: 8000000 INFO @ Sat, 11 Dec 2021 06:40:38: 19000000 INFO @ Sat, 11 Dec 2021 06:40:42: 14000000 INFO @ Sat, 11 Dec 2021 06:40:43: 9000000 INFO @ Sat, 11 Dec 2021 06:40:44: 20000000 INFO @ Sat, 11 Dec 2021 06:40:47: 15000000 INFO @ Sat, 11 Dec 2021 06:40:49: 10000000 INFO @ Sat, 11 Dec 2021 06:40:50: 21000000 INFO @ Sat, 11 Dec 2021 06:40:53: 16000000 INFO @ Sat, 11 Dec 2021 06:40:55: 11000000 INFO @ Sat, 11 Dec 2021 06:40:55: 22000000 INFO @ Sat, 11 Dec 2021 06:40:56: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:40:56: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:40:56: #1 total tags in treatment: 22144109 INFO @ Sat, 11 Dec 2021 06:40:56: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:40:56: #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 06:40:57: #1 tags after filtering in treatment: 22144109 INFO @ Sat, 11 Dec 2021 06:40:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:40:57: #1 finished! INFO @ Sat, 11 Dec 2021 06:40:57: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:40:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:40:58: #2 number of paired peaks: 392 WARNING @ Sat, 11 Dec 2021 06:40:58: Fewer paired peaks (392) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 392 pairs to build model! INFO @ Sat, 11 Dec 2021 06:40:58: start model_add_line... INFO @ Sat, 11 Dec 2021 06:40:58: start X-correlation... INFO @ Sat, 11 Dec 2021 06:40:58: end of X-cor INFO @ Sat, 11 Dec 2021 06:40:58: #2 finished! INFO @ Sat, 11 Dec 2021 06:40:58: #2 predicted fragment length is 110 bps INFO @ Sat, 11 Dec 2021 06:40:58: #2 alternative fragment length(s) may be 110 bps INFO @ Sat, 11 Dec 2021 06:40:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720903/SRX9720903.05_model.r INFO @ Sat, 11 Dec 2021 06:40:58: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:40:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:40:59: 17000000 INFO @ Sat, 11 Dec 2021 06:41:00: 12000000 INFO @ Sat, 11 Dec 2021 06:41:04: 18000000 INFO @ Sat, 11 Dec 2021 06:41:06: 13000000 INFO @ Sat, 11 Dec 2021 06:41:10: 19000000 INFO @ Sat, 11 Dec 2021 06:41:11: 14000000 INFO @ Sat, 11 Dec 2021 06:41:16: 20000000 INFO @ Sat, 11 Dec 2021 06:41:17: 15000000 INFO @ Sat, 11 Dec 2021 06:41:22: 21000000 INFO @ Sat, 11 Dec 2021 06:41:23: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 06:41:27: 22000000 INFO @ Sat, 11 Dec 2021 06:41:28: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:41:28: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:41:28: #1 total tags in treatment: 22144109 INFO @ Sat, 11 Dec 2021 06:41:28: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:41:28: #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 06:41:28: 17000000 INFO @ Sat, 11 Dec 2021 06:41:29: #1 tags after filtering in treatment: 22144109 INFO @ Sat, 11 Dec 2021 06:41:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:41:29: #1 finished! INFO @ Sat, 11 Dec 2021 06:41:29: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:41:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:41:30: #2 number of paired peaks: 392 WARNING @ Sat, 11 Dec 2021 06:41:30: Fewer paired peaks (392) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 392 pairs to build model! INFO @ Sat, 11 Dec 2021 06:41:30: start model_add_line... INFO @ Sat, 11 Dec 2021 06:41:30: start X-correlation... INFO @ Sat, 11 Dec 2021 06:41:30: end of X-cor INFO @ Sat, 11 Dec 2021 06:41:30: #2 finished! INFO @ Sat, 11 Dec 2021 06:41:30: #2 predicted fragment length is 110 bps INFO @ Sat, 11 Dec 2021 06:41:30: #2 alternative fragment length(s) may be 110 bps INFO @ Sat, 11 Dec 2021 06:41:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720903/SRX9720903.10_model.r INFO @ Sat, 11 Dec 2021 06:41:30: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:41:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:41:34: 18000000 INFO @ Sat, 11 Dec 2021 06:41:39: 19000000 INFO @ Sat, 11 Dec 2021 06:41:40: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:41:44: 20000000 INFO @ Sat, 11 Dec 2021 06:41:50: 21000000 INFO @ Sat, 11 Dec 2021 06:41:55: 22000000 INFO @ Sat, 11 Dec 2021 06:41:56: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:41:56: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:41:56: #1 total tags in treatment: 22144109 INFO @ Sat, 11 Dec 2021 06:41:56: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:41:56: #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 06:41:56: #1 tags after filtering in treatment: 22144109 INFO @ Sat, 11 Dec 2021 06:41:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:41:56: #1 finished! INFO @ Sat, 11 Dec 2021 06:41:56: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:41:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:41:58: #2 number of paired peaks: 392 WARNING @ Sat, 11 Dec 2021 06:41:58: Fewer paired peaks (392) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 392 pairs to build model! INFO @ Sat, 11 Dec 2021 06:41:58: start model_add_line... INFO @ Sat, 11 Dec 2021 06:41:58: start X-correlation... INFO @ Sat, 11 Dec 2021 06:41:58: end of X-cor INFO @ Sat, 11 Dec 2021 06:41:58: #2 finished! INFO @ Sat, 11 Dec 2021 06:41:58: #2 predicted fragment length is 110 bps INFO @ Sat, 11 Dec 2021 06:41:58: #2 alternative fragment length(s) may be 110 bps INFO @ Sat, 11 Dec 2021 06:41:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720903/SRX9720903.20_model.r INFO @ Sat, 11 Dec 2021 06:41:58: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:41:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:42:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720903/SRX9720903.05_peaks.xls INFO @ Sat, 11 Dec 2021 06:42:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720903/SRX9720903.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:42:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720903/SRX9720903.05_summits.bed INFO @ Sat, 11 Dec 2021 06:42:00: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6202 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:42:09: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 06:42:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720903/SRX9720903.10_peaks.xls INFO @ Sat, 11 Dec 2021 06:42:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720903/SRX9720903.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:42:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720903/SRX9720903.10_summits.bed INFO @ Sat, 11 Dec 2021 06:42:28: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4271 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:42:39: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:42:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720903/SRX9720903.20_peaks.xls INFO @ Sat, 11 Dec 2021 06:42:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720903/SRX9720903.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:42:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720903/SRX9720903.20_summits.bed INFO @ Sat, 11 Dec 2021 06:42:58: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2626 records, 4 fields): 16 millis CompletedMACS2peakCalling