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-rw-r--r--bh20sequploader/main.py5
-rw-r--r--bh20sequploader/qc_fasta.py9
2 files changed, 8 insertions, 6 deletions
diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py
index f89b458..ea0fa70 100644
--- a/bh20sequploader/main.py
+++ b/bh20sequploader/main.py
@@ -49,7 +49,7 @@ sequence for enough overlap with the reference genome
failed = True
except Exception as e:
log.exception("Failed metadata QC")
- failed = True
+ failed = True # continue with the FASTA checker
target = []
try:
@@ -64,13 +64,14 @@ sequence for enough overlap with the reference genome
target[1] = ("reads_2."+target[1][0][6:], target[1][1], target[1][2])
if do_qc and target[0][2] == 'text/fasta' and sample_id != target[0][1]:
- raise ValueError("The sample_id field in the metadata must be the same as the FASTA header")
+ raise ValueError(f"The sample_id field in the metadata ({sample_id}) must be the same as the FASTA header ({target[0][1]})")
except Exception as e:
log.exception("Failed sequence QC")
failed = True
if failed:
+ log.debug("Bailing out!")
exit(1)
return target
diff --git a/bh20sequploader/qc_fasta.py b/bh20sequploader/qc_fasta.py
index f567f0a..814fb3e 100644
--- a/bh20sequploader/qc_fasta.py
+++ b/bh20sequploader/qc_fasta.py
@@ -66,7 +66,8 @@ def qc_fasta(arg_sequence, check_with_mimimap2=True):
similarity = 0
try:
- cmd = ["minimap2", "-c -x asm20", tmp1.name, tmp2.name]
+ log.debug("Trying to run minimap2")
+ cmd = ["minimap2", "-c", "-x", "asm20", tmp1.name, tmp2.name]
logging.info("QC checking similarity to reference")
logging.info(" ".join(cmd))
result = subprocess.run(cmd, stdout=subprocess.PIPE)
@@ -83,9 +84,7 @@ def qc_fasta(arg_sequence, check_with_mimimap2=True):
if similarity < 70.0:
raise ValueError(
- "QC fail for {}: alignment to reference was less than 70%% (was %2.2f%%)".format(
- seqlabel, similarity
- ))
+ f"QC fail for {seqlabel}: alignment to reference was less than 70% (was {similarity})")
return "sequence.fasta" + gz, seqlabel, seq_type
elif seq_type == "text/fastq":
@@ -93,4 +92,6 @@ def qc_fasta(arg_sequence, check_with_mimimap2=True):
sequence.detach()
return "reads.fastq" + gz, seqlabel, seq_type
else:
+ log.debug(seqlabel)
+ log.debug(seq_type)
raise ValueError("Sequence file ({}) does not look like a DNA FASTA or FASTQ".format(arg_sequence))