Job ID = 16440186 SRX = SRX15369007 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T08:31:12 prefetch.2.10.7: 1) Downloading 'SRR19308736'... 2022-08-02T08:31:12 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T08:32:07 prefetch.2.10.7: HTTPS download succeed 2022-08-02T08:32:07 prefetch.2.10.7: 1) 'SRR19308736' was downloaded successfully 2022-08-02T08:32:07 prefetch.2.10.7: 'SRR19308736' has 0 unresolved dependencies Read 26419843 spots for SRR19308736/SRR19308736.sra Written 26419843 spots for SRR19308736/SRR19308736.sra fastq に変換しました。 bowtie でマッピング中... Your job 16440848 ("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: 00:20:35 26419843 reads; of these: 26419843 (100.00%) were unpaired; of these: 890890 (3.37%) aligned 0 times 17620370 (66.69%) aligned exactly 1 time 7908583 (29.93%) aligned >1 times 96.63% overall alignment rate Time searching: 00:20:35 Overall time: 00:20:35 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 12 files... [bam_rmdupse_core] 9951844 / 25528953 = 0.3898 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 18:05:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15369007/SRX15369007.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15369007/SRX15369007.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15369007/SRX15369007.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15369007/SRX15369007.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 18:05:04: #1 read tag files... INFO @ Tue, 02 Aug 2022 18:05:04: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 18:05:15: 1000000 INFO @ Tue, 02 Aug 2022 18:05:25: 2000000 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 18:05:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15369007/SRX15369007.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15369007/SRX15369007.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15369007/SRX15369007.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15369007/SRX15369007.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 18:05:32: #1 read tag files... INFO @ Tue, 02 Aug 2022 18:05:32: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 18:05:36: 3000000 INFO @ Tue, 02 Aug 2022 18:05:41: 1000000 INFO @ Tue, 02 Aug 2022 18:05:46: 4000000 INFO @ Tue, 02 Aug 2022 18:05:51: 2000000 INFO @ Tue, 02 Aug 2022 18:05:57: 5000000 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 18:06:00: 3000000 INFO @ Tue, 02 Aug 2022 18:06:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15369007/SRX15369007.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15369007/SRX15369007.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15369007/SRX15369007.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15369007/SRX15369007.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 18:06:02: #1 read tag files... INFO @ Tue, 02 Aug 2022 18:06:02: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 18:06:08: 6000000 INFO @ Tue, 02 Aug 2022 18:06:10: 4000000 INFO @ Tue, 02 Aug 2022 18:06:12: 1000000 INFO @ Tue, 02 Aug 2022 18:06:19: 7000000 INFO @ Tue, 02 Aug 2022 18:06:20: 5000000 INFO @ Tue, 02 Aug 2022 18:06:22: 2000000 INFO @ Tue, 02 Aug 2022 18:06:29: 6000000 INFO @ Tue, 02 Aug 2022 18:06:29: 8000000 INFO @ Tue, 02 Aug 2022 18:06:32: 3000000 INFO @ Tue, 02 Aug 2022 18:06:39: 7000000 INFO @ Tue, 02 Aug 2022 18:06:40: 9000000 INFO @ Tue, 02 Aug 2022 18:06:41: 4000000 INFO @ Tue, 02 Aug 2022 18:06:49: 8000000 INFO @ Tue, 02 Aug 2022 18:06:51: 5000000 INFO @ Tue, 02 Aug 2022 18:06:51: 10000000 INFO @ Tue, 02 Aug 2022 18:06:59: 9000000 INFO @ Tue, 02 Aug 2022 18:07:00: 6000000 INFO @ Tue, 02 Aug 2022 18:07:01: 11000000 INFO @ Tue, 02 Aug 2022 18:07:10: 10000000 INFO @ Tue, 02 Aug 2022 18:07:11: 7000000 INFO @ Tue, 02 Aug 2022 18:07:12: 12000000 INFO @ Tue, 02 Aug 2022 18:07:19: 11000000 INFO @ Tue, 02 Aug 2022 18:07:21: 8000000 INFO @ Tue, 02 Aug 2022 18:07:23: 13000000 INFO @ Tue, 02 Aug 2022 18:07:29: 12000000 INFO @ Tue, 02 Aug 2022 18:07:31: 9000000 INFO @ Tue, 02 Aug 2022 18:07:33: 14000000 INFO @ Tue, 02 Aug 2022 18:07:39: 13000000 INFO @ Tue, 02 Aug 2022 18:07:41: 10000000 INFO @ Tue, 02 Aug 2022 18:07:44: 15000000 INFO @ Tue, 02 Aug 2022 18:07:49: 14000000 INFO @ Tue, 02 Aug 2022 18:07:50: 11000000 INFO @ Tue, 02 Aug 2022 18:07:50: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 18:07:50: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 18:07:50: #1 total tags in treatment: 15577109 INFO @ Tue, 02 Aug 2022 18:07:50: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 18:07:50: #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 18:07:51: #1 tags after filtering in treatment: 15577109 INFO @ Tue, 02 Aug 2022 18:07:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 18:07:51: #1 finished! INFO @ Tue, 02 Aug 2022 18:07:51: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 18:07:51: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 18:07:52: #2 number of paired peaks: 237 WARNING @ Tue, 02 Aug 2022 18:07:52: Fewer paired peaks (237) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 237 pairs to build model! INFO @ Tue, 02 Aug 2022 18:07:52: start model_add_line... INFO @ Tue, 02 Aug 2022 18:07:52: start X-correlation... INFO @ Tue, 02 Aug 2022 18:07:52: end of X-cor INFO @ Tue, 02 Aug 2022 18:07:52: #2 finished! INFO @ Tue, 02 Aug 2022 18:07:52: #2 predicted fragment length is 139 bps INFO @ Tue, 02 Aug 2022 18:07:52: #2 alternative fragment length(s) may be 139 bps INFO @ Tue, 02 Aug 2022 18:07:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15369007/SRX15369007.05_model.r WARNING @ Tue, 02 Aug 2022 18:07:52: #2 Since the d (139) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 18:07:52: #2 You may need to consider one of the other alternative d(s): 139 WARNING @ Tue, 02 Aug 2022 18:07:52: #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 18:07:52: #3 Call peaks... INFO @ Tue, 02 Aug 2022 18:07:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 18:07:58: 15000000 INFO @ Tue, 02 Aug 2022 18:07:59: 12000000 INFO @ Tue, 02 Aug 2022 18:08:03: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 18:08:03: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 18:08:03: #1 total tags in treatment: 15577109 INFO @ Tue, 02 Aug 2022 18:08:03: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 18:08:03: #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 18:08:04: #1 tags after filtering in treatment: 15577109 INFO @ Tue, 02 Aug 2022 18:08:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 18:08:04: #1 finished! INFO @ Tue, 02 Aug 2022 18:08:04: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 18:08:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 18:08:05: #2 number of paired peaks: 237 WARNING @ Tue, 02 Aug 2022 18:08:05: Fewer paired peaks (237) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 237 pairs to build model! INFO @ Tue, 02 Aug 2022 18:08:05: start model_add_line... INFO @ Tue, 02 Aug 2022 18:08:05: start X-correlation... INFO @ Tue, 02 Aug 2022 18:08:05: end of X-cor INFO @ Tue, 02 Aug 2022 18:08:05: #2 finished! INFO @ Tue, 02 Aug 2022 18:08:05: #2 predicted fragment length is 139 bps INFO @ Tue, 02 Aug 2022 18:08:05: #2 alternative fragment length(s) may be 139 bps INFO @ Tue, 02 Aug 2022 18:08:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15369007/SRX15369007.10_model.r WARNING @ Tue, 02 Aug 2022 18:08:05: #2 Since the d (139) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 18:08:05: #2 You may need to consider one of the other alternative d(s): 139 WARNING @ Tue, 02 Aug 2022 18:08:05: #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 18:08:05: #3 Call peaks... INFO @ Tue, 02 Aug 2022 18:08:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 18:08:09: 13000000 INFO @ Tue, 02 Aug 2022 18:08:17: 14000000 INFO @ Tue, 02 Aug 2022 18:08:26: 15000000 INFO @ Tue, 02 Aug 2022 18:08:31: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 18:08:31: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 18:08:31: #1 total tags in treatment: 15577109 INFO @ Tue, 02 Aug 2022 18:08:31: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 18:08:31: #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 18:08:31: #1 tags after filtering in treatment: 15577109 INFO @ Tue, 02 Aug 2022 18:08:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 18:08:31: #1 finished! INFO @ Tue, 02 Aug 2022 18:08:31: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 18:08:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 18:08:32: #2 number of paired peaks: 237 WARNING @ Tue, 02 Aug 2022 18:08:32: Fewer paired peaks (237) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 237 pairs to build model! INFO @ Tue, 02 Aug 2022 18:08:32: start model_add_line... INFO @ Tue, 02 Aug 2022 18:08:33: start X-correlation... INFO @ Tue, 02 Aug 2022 18:08:33: end of X-cor INFO @ Tue, 02 Aug 2022 18:08:33: #2 finished! INFO @ Tue, 02 Aug 2022 18:08:33: #2 predicted fragment length is 139 bps INFO @ Tue, 02 Aug 2022 18:08:33: #2 alternative fragment length(s) may be 139 bps INFO @ Tue, 02 Aug 2022 18:08:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15369007/SRX15369007.20_model.r WARNING @ Tue, 02 Aug 2022 18:08:33: #2 Since the d (139) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 18:08:33: #2 You may need to consider one of the other alternative d(s): 139 WARNING @ Tue, 02 Aug 2022 18:08:33: #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 18:08:33: #3 Call peaks... INFO @ Tue, 02 Aug 2022 18:08:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 18:08:36: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 18:08:48: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 18:08:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15369007/SRX15369007.05_peaks.xls INFO @ Tue, 02 Aug 2022 18:08:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15369007/SRX15369007.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 18:08:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15369007/SRX15369007.05_summits.bed INFO @ Tue, 02 Aug 2022 18:08:59: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (12429 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 18:09:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15369007/SRX15369007.10_peaks.xls INFO @ Tue, 02 Aug 2022 18:09:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15369007/SRX15369007.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 18:09:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15369007/SRX15369007.10_summits.bed INFO @ Tue, 02 Aug 2022 18:09:12: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (6782 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 18:09:16: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 18:09:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15369007/SRX15369007.20_peaks.xls INFO @ Tue, 02 Aug 2022 18:09:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15369007/SRX15369007.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 18:09:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15369007/SRX15369007.20_summits.bed INFO @ Tue, 02 Aug 2022 18:09:39: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2494 records, 4 fields): 26 millis CompletedMACS2peakCalling