Hello Everyone,
I am trying to run archer analysis pipeline from command prompt, but when I write command "$ archer/archer.pl -config config.dat" it will display following error.
can anyone tell me how to execute the archer via command prompt and how to solve this error.?
Align Reads
sh: 2: bwa_enz: not found
test2
Rename SAM Files
mv: cannot stat `/home/plus91/command//test2.fastq.sam': No such file or directory
Alignments
[main_samview] fail to open "/home/plus91/command//test2.sam.full" for reading.
[samopen] no @SQ lines in the header.
[sam_read1] missing header? Abort!
De-duplication
Traceback (most recent call last):
File "/home/plus91/archer_1.0.0/archer/get_median_quality.py", line 32, in <module>
for read in reader:
File "/usr/local/lib/python2.7/dist-packages/HTSeq-0.6.1p1-py2.7-linux-x86_64.egg/HTSeq/__init__.py", line 394, in __iter__
raise ValueError( "Primary and secondary ID line in FASTQ"
ValueError: Primary and secondary ID line in FASTQdisagree.
Can't open /home/plus91/command//test2.sam.full : No such file or directory at /home/plus91/archer_1.0.0/archer/de_dup_2_hash.pl line 60.
Select On- and Off-target Reads
Error: The requested bed file (/home/plus91/command//test2.points.bed) could not be opened. Exiting!
Error: The requested bed file (/home/plus91/command//test2.dedup.points.bed) could not be opened. Exiting!
Generate Coverage and Start Sites
[bam_header_read] EOF marker is absent. The input is probably truncated.
[samfaipath] fail to read file /archer_1.0.0/chromFa/hg19.fa.
[main_samview] fail to open "/dev/stdin" for reading.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
BamHeader ERROR: could not read magic number
BamReader ERROR: Could not load header data for /dev/stdin
[bam_header_read] EOF marker is absent. The input is probably truncated.
[samopen] no @SQ lines in the header.
[sam_read1] missing header? Abort!
Generate Master Files
Traceback (most recent call last):
File "/home/plus91/archer_1.0.0/archer/archer/annotation/annotate.py", line 286, in <module>
main(argv)
File "/home/plus91/archer_1.0.0/archer/archer/annotation/annotate.py", line 274, in main
chromosomes, gene_spans = gtf_to_gene(open(opts.gtf_file, 'U'))
IOError: [Errno 2] No such file or directory: '/archer_1.0.0/hg19_annotations.gtf'
Can't open /home/plus91/command//test2.dedup.prejoin.master.dat : No such file or directory at /home/plus91/archer_1.0.0/archer/join_master_file.pl line 32.
Select Fusion Reads
Count Fusions and Splice Events
Can't open /archer_1.0.0/hg19_annotations.gtf : No such file or directory at /home/plus91/archer_1.0.0/archer/count_fusions.pl line 233.
Can't open /archer_1.0.0/hg19_annotations.gtf : No such file or directory at /home/plus91/archer_1.0.0/archer/count_fusions.pl line 233.
Can't open /home/plus91/command//test2.fusion_counts_bare.dat : No such file or directory at /home/plus91/archer_1.0.0/archer/add_splice_to_fusion_counts.pl line 26.
Flanking Sequences
Can't open /home/plus91/command//test2.fusion_counts_bare.dat : No such file or directory at /home/plus91/archer_1.0.0/archer/flanking_sequences.pl line 28.
Can't open /home/plus91/command//test2.splice_counts_bare.dat : No such file or directory at /home/plus91/archer_1.0.0/archer/flanking_sequences.pl line 28.
BAM Dedup Files
[samopen] no @SQ lines in the header.
[sam_read1] missing header? Abort!
[bam_header_read] EOF marker is absent. The input is probably truncated.
Sort SAM Files
[main_samview] fail to open "/home/plus91/command//test2.sam.full" for reading.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
Segmentation fault (core dumped)
open: No such file or directory
[main_samview] fail to open "/home/plus91/command//test2.bam.full.prefix.bam" for reading.
[samopen] no @SQ lines in the header.
[sam_read1] missing header? Abort!
[bam_header_read] EOF marker is absent. The input is probably truncated.
On-target Stats
Total Molecule Counts
De-duplicated Molecule Counts
All Molecule Counts
Can't open /home/plus91/command//test2.on_target.dat : No such file or directory at /home/plus91/archer_1.0.0/archer/counts_2.pl line 65.
QC Check
Coverage Uniformity
Summary
cat: /home/plus91/command//test2.counts.dat: No such file or directory
cat: /home/plus91/command//test2.fusion_counts_with_splice_bare.dat: No such file or directory
cat: /home/plus91/command//test2.counts.machine.dat: No such file or directory
cat: /home/plus91/command//test2.fusion_counts_with_splice_bare.machine.dat: No such file or directory
Clean Up
Can't open /home/plus91/command//test2.flanking_sequences.dat : No such file or directory at /home/plus91/archer_1.0.0/archer/clean_up_flanking_sequences.pl line 23.
Can't open /home/plus91/command//test2.flanking_splice_sequences.dat : No such file or directory at /home/plus91/archer_1.0.0/archer/clean_up_flanking_sequences.pl line 23.
rm: cannot remove `/home/plus91/command//test2.sam.full': No such file or directory
rm: cannot remove `/home/plus91/command//test2.dedup.prejoin.master.dat': No such file or directory
rm: cannot remove `/home/plus91/command//test2.fusion_counts.dat': No such file or directory
rm: cannot remove `/home/plus91/command//test2.fusion_counts_bare.dat': No such file or directory
rm: cannot remove `/home/plus91/command//test2.splice_counts.dat': No such file or directory
rm: cannot remove `/home/plus91/command//test2.splice_counts_bare.dat': No such file or directory
rm: cannot remove `/home/plus91/command//test2.fusion_counts_with_splice_bare.dat': No such file or directory
rm: cannot remove `/home/plus91/command//test2.fusion_counts_with_splice_bare.machine.dat': No such file or directory
rm: cannot remove `/home/plus91/command//test2.housekeeping.dedup.dat': No such file or directory
rm: cannot remove `/home/plus91/command//test2.dedup.on_target.dat': No such file or directory
rm: cannot remove `/home/plus91/command//test2.dedup.reads_per_exon.dat': No such file or directory
rm: cannot remove `/home/plus91/command//test2.dedup.reads_per_exon.machine.dat': No such file or directory
rm: cannot remove `/home/plus91/command//test2.housekeeping.dat': No such file or directory
rm: cannot remove `/home/plus91/command//test2.on_target.dat': No such file or directory
rm: cannot remove `/home/plus91/command//test2.reads_per_exon.dat': No such file or directory
rm: cannot remove `/home/plus91/command//test2.bam.full.prefix.bam': No such file or directory
rm: cannot remove `/home/plus91/command//test2.counts.dat': No such file or directory
rm: cannot remove `/home/plus91/command//test2.counts.machine.dat': No such file or directory
Thank You.
Shirish
