Job ID = 16439748 SRX = SRX14894237 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T07:05:07 prefetch.2.10.7: 1) Downloading 'SRR18795784'... 2022-08-02T07:05:07 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T07:05:43 prefetch.2.10.7: HTTPS download succeed 2022-08-02T07:05:43 prefetch.2.10.7: 1) 'SRR18795784' was downloaded successfully 2022-08-02T07:05:43 prefetch.2.10.7: 'SRR18795784' has 0 unresolved dependencies Read 26576972 spots for SRR18795784/SRR18795784.sra Written 26576972 spots for SRR18795784/SRR18795784.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439869 ("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: 00:12:52 26576972 reads; of these: 26576972 (100.00%) were unpaired; of these: 2368346 (8.91%) aligned 0 times 17418095 (65.54%) aligned exactly 1 time 6790531 (25.55%) aligned >1 times 91.09% overall alignment rate Time searching: 00:12:52 Overall time: 00:12:52 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] 18061108 / 24208626 = 0.7461 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 16:27:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14894237/SRX14894237.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14894237/SRX14894237.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14894237/SRX14894237.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14894237/SRX14894237.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 16:27:31: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:27:31: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:27:39: 1000000 INFO @ Tue, 02 Aug 2022 16:27:49: 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 16:27:57: 3000000 INFO @ Tue, 02 Aug 2022 16:27:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14894237/SRX14894237.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14894237/SRX14894237.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14894237/SRX14894237.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14894237/SRX14894237.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 16:27:59: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:27:59: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:28:06: 4000000 INFO @ Tue, 02 Aug 2022 16:28:09: 1000000 INFO @ Tue, 02 Aug 2022 16:28:15: 5000000 INFO @ Tue, 02 Aug 2022 16:28:19: 2000000 INFO @ Tue, 02 Aug 2022 16:28:23: 6000000 INFO @ Tue, 02 Aug 2022 16:28:25: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 16:28:25: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 16:28:25: #1 total tags in treatment: 6147518 INFO @ Tue, 02 Aug 2022 16:28:25: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:28:25: #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 16:28:25: #1 tags after filtering in treatment: 6147518 INFO @ Tue, 02 Aug 2022 16:28:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:28:25: #1 finished! INFO @ Tue, 02 Aug 2022 16:28:25: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:28:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:28:26: #2 number of paired peaks: 2476 INFO @ Tue, 02 Aug 2022 16:28:26: start model_add_line... INFO @ Tue, 02 Aug 2022 16:28:26: start X-correlation... INFO @ Tue, 02 Aug 2022 16:28:26: end of X-cor INFO @ Tue, 02 Aug 2022 16:28:26: #2 finished! INFO @ Tue, 02 Aug 2022 16:28:26: #2 predicted fragment length is 78 bps INFO @ Tue, 02 Aug 2022 16:28:26: #2 alternative fragment length(s) may be 78 bps INFO @ Tue, 02 Aug 2022 16:28:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14894237/SRX14894237.05_model.r WARNING @ Tue, 02 Aug 2022 16:28:26: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 16:28:26: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Tue, 02 Aug 2022 16:28:26: #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 16:28:26: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:28:26: #3 Pre-compute pvalue-qvalue table... 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 16:28:28: 3000000 INFO @ Tue, 02 Aug 2022 16:28:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14894237/SRX14894237.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14894237/SRX14894237.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14894237/SRX14894237.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14894237/SRX14894237.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 16:28:29: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:28:29: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:28:36: 4000000 INFO @ Tue, 02 Aug 2022 16:28:39: 1000000 INFO @ Tue, 02 Aug 2022 16:28:45: 5000000 INFO @ Tue, 02 Aug 2022 16:28:46: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:28:48: 2000000 INFO @ Tue, 02 Aug 2022 16:28:54: 6000000 INFO @ Tue, 02 Aug 2022 16:28:55: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 16:28:55: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 16:28:55: #1 total tags in treatment: 6147518 INFO @ Tue, 02 Aug 2022 16:28:55: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:28:55: #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 16:28:55: #1 tags after filtering in treatment: 6147518 INFO @ Tue, 02 Aug 2022 16:28:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:28:55: #1 finished! INFO @ Tue, 02 Aug 2022 16:28:55: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:28:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:28:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14894237/SRX14894237.05_peaks.xls INFO @ Tue, 02 Aug 2022 16:28:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14894237/SRX14894237.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:28:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14894237/SRX14894237.05_summits.bed INFO @ Tue, 02 Aug 2022 16:28:56: #2 number of paired peaks: 2476 INFO @ Tue, 02 Aug 2022 16:28:56: start model_add_line... INFO @ Tue, 02 Aug 2022 16:28:56: Done! INFO @ Tue, 02 Aug 2022 16:28:56: start X-correlation... INFO @ Tue, 02 Aug 2022 16:28:56: end of X-cor INFO @ Tue, 02 Aug 2022 16:28:56: #2 finished! INFO @ Tue, 02 Aug 2022 16:28:56: #2 predicted fragment length is 78 bps INFO @ Tue, 02 Aug 2022 16:28:56: #2 alternative fragment length(s) may be 78 bps INFO @ Tue, 02 Aug 2022 16:28:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14894237/SRX14894237.10_model.r WARNING @ Tue, 02 Aug 2022 16:28:56: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 16:28:56: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Tue, 02 Aug 2022 16:28:56: #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 16:28:56: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:28:56: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3680 records, 4 fields): 58 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:28:57: 3000000 INFO @ Tue, 02 Aug 2022 16:29:05: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 16:29:14: 5000000 INFO @ Tue, 02 Aug 2022 16:29:16: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:29:22: 6000000 INFO @ Tue, 02 Aug 2022 16:29:24: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 16:29:24: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 16:29:24: #1 total tags in treatment: 6147518 INFO @ Tue, 02 Aug 2022 16:29:24: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:29:24: #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 16:29:24: #1 tags after filtering in treatment: 6147518 INFO @ Tue, 02 Aug 2022 16:29:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:29:24: #1 finished! INFO @ Tue, 02 Aug 2022 16:29:24: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:29:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:29:25: #2 number of paired peaks: 2476 INFO @ Tue, 02 Aug 2022 16:29:25: start model_add_line... INFO @ Tue, 02 Aug 2022 16:29:25: start X-correlation... INFO @ Tue, 02 Aug 2022 16:29:25: end of X-cor INFO @ Tue, 02 Aug 2022 16:29:25: #2 finished! INFO @ Tue, 02 Aug 2022 16:29:25: #2 predicted fragment length is 78 bps INFO @ Tue, 02 Aug 2022 16:29:25: #2 alternative fragment length(s) may be 78 bps INFO @ Tue, 02 Aug 2022 16:29:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14894237/SRX14894237.20_model.r WARNING @ Tue, 02 Aug 2022 16:29:25: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 16:29:25: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Tue, 02 Aug 2022 16:29:25: #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 16:29:25: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:29:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:29:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14894237/SRX14894237.10_peaks.xls INFO @ Tue, 02 Aug 2022 16:29:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14894237/SRX14894237.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:29:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14894237/SRX14894237.10_summits.bed INFO @ Tue, 02 Aug 2022 16:29:26: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1914 records, 4 fields): 62 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 16:29:45: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:29:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14894237/SRX14894237.20_peaks.xls INFO @ Tue, 02 Aug 2022 16:29:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14894237/SRX14894237.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:29:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14894237/SRX14894237.20_summits.bed INFO @ Tue, 02 Aug 2022 16:29:56: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (893 records, 4 fields): 400 millis CompletedMACS2peakCalling