[2024-01-24 14:13:01,669] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:13:01,676] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:13:01,676] [INFO] DQC Reference Directory: /var/lib/cwl/stgc3ad6268-90b1-4389-9f53-87f51557e4aa/dqc_reference
[2024-01-24 14:13:02,871] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:13:02,872] [INFO] Task started: Prodigal
[2024-01-24 14:13:02,872] [INFO] Running command: gunzip -c /var/lib/cwl/stgf000eecf-bfb2-4a1d-ba2f-5f89f911fa0b/GCF_900445495.1_52683_B04_genomic.fna.gz | prodigal -d GCF_900445495.1_52683_B04_genomic.fna/cds.fna -a GCF_900445495.1_52683_B04_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:13:26,044] [INFO] Task succeeded: Prodigal
[2024-01-24 14:13:26,045] [INFO] Task started: HMMsearch
[2024-01-24 14:13:26,045] [INFO] Running command: hmmsearch --tblout GCF_900445495.1_52683_B04_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc3ad6268-90b1-4389-9f53-87f51557e4aa/dqc_reference/reference_markers.hmm GCF_900445495.1_52683_B04_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:13:26,358] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:13:26,360] [INFO] Found 6/6 markers.
[2024-01-24 14:13:26,405] [INFO] Query marker FASTA was written to GCF_900445495.1_52683_B04_genomic.fna/markers.fasta
[2024-01-24 14:13:26,405] [INFO] Task started: Blastn
[2024-01-24 14:13:26,406] [INFO] Running command: blastn -query GCF_900445495.1_52683_B04_genomic.fna/markers.fasta -db /var/lib/cwl/stgc3ad6268-90b1-4389-9f53-87f51557e4aa/dqc_reference/reference_markers.fasta -out GCF_900445495.1_52683_B04_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:27,114] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:27,118] [INFO] Selected 8 target genomes.
[2024-01-24 14:13:27,119] [INFO] Target genome list was writen to GCF_900445495.1_52683_B04_genomic.fna/target_genomes.txt
[2024-01-24 14:13:27,125] [INFO] Task started: fastANI
[2024-01-24 14:13:27,125] [INFO] Running command: fastANI --query /var/lib/cwl/stgf000eecf-bfb2-4a1d-ba2f-5f89f911fa0b/GCF_900445495.1_52683_B04_genomic.fna.gz --refList GCF_900445495.1_52683_B04_genomic.fna/target_genomes.txt --output GCF_900445495.1_52683_B04_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:36,168] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:36,168] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc3ad6268-90b1-4389-9f53-87f51557e4aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:36,169] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc3ad6268-90b1-4389-9f53-87f51557e4aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:36,177] [INFO] Found 8 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:13:36,177] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:13:36,177] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Parabacteroides merdae	strain=NCTC13052	GCA_900445495.1	46503	46503	type	True	100.0	1462	1467	95	conclusive
Parabacteroides merdae	strain=ATCC 43184	GCA_025151215.1	46503	46503	type	True	99.9985	1454	1467	95	conclusive
Parabacteroides merdae	strain=ATCC 43184	GCA_000154105.1	46503	46503	type	True	99.9842	1431	1467	95	conclusive
Parabacteroides johnsonii	strain=DSM 18315	GCA_025151045.1	387661	387661	type	True	91.1243	1106	1467	95	below_threshold
Parabacteroides johnsonii	strain=DSM 18315	GCA_000156495.1	387661	387661	type	True	90.9078	1098	1467	95	below_threshold
Phocaeicola faecalis	strain=FXJYN30E22	GCA_021730445.1	2786956	2786956	type	True	80.8502	100	1467	95	below_threshold
Phocaeicola intestinalis	strain=Sa1CVN1	GCA_014837065.1	2762212	2762212	type	True	79.8724	74	1467	95	below_threshold
Bacteroides muris	strain=KH365_2	GCA_024704915.1	2937417	2937417	type	True	79.6642	96	1467	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:36,179] [INFO] DFAST Taxonomy check result was written to GCF_900445495.1_52683_B04_genomic.fna/tc_result.tsv
[2024-01-24 14:13:36,180] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:36,181] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:36,181] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc3ad6268-90b1-4389-9f53-87f51557e4aa/dqc_reference/checkm_data
[2024-01-24 14:13:36,183] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:36,228] [INFO] Task started: CheckM
[2024-01-24 14:13:36,229] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900445495.1_52683_B04_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900445495.1_52683_B04_genomic.fna/checkm_input GCF_900445495.1_52683_B04_genomic.fna/checkm_result
[2024-01-24 14:14:41,190] [INFO] Task succeeded: CheckM
[2024-01-24 14:14:41,191] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:14:41,216] [INFO] ===== Completeness check finished =====
[2024-01-24 14:14:41,216] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:14:41,217] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900445495.1_52683_B04_genomic.fna/markers.fasta)
[2024-01-24 14:14:41,217] [INFO] Task started: Blastn
[2024-01-24 14:14:41,217] [INFO] Running command: blastn -query GCF_900445495.1_52683_B04_genomic.fna/markers.fasta -db /var/lib/cwl/stgc3ad6268-90b1-4389-9f53-87f51557e4aa/dqc_reference/reference_markers_gtdb.fasta -out GCF_900445495.1_52683_B04_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:42,002] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:42,006] [INFO] Selected 10 target genomes.
[2024-01-24 14:14:42,006] [INFO] Target genome list was writen to GCF_900445495.1_52683_B04_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:14:42,018] [INFO] Task started: fastANI
[2024-01-24 14:14:42,018] [INFO] Running command: fastANI --query /var/lib/cwl/stgf000eecf-bfb2-4a1d-ba2f-5f89f911fa0b/GCF_900445495.1_52683_B04_genomic.fna.gz --refList GCF_900445495.1_52683_B04_genomic.fna/target_genomes_gtdb.txt --output GCF_900445495.1_52683_B04_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:14:52,241] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:52,257] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:14:52,257] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_000154105.1	s__Parabacteroides merdae	99.9842	1431	1467	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.97	97.44	0.89	0.77	85	conclusive
GCF_000156495.1	s__Parabacteroides johnsonii	90.9078	1098	1467	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.42	96.67	0.88	0.77	13	-
GCF_014287585.1	s__Parabacteroides sp014287585	89.8761	1065	1467	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.33	98.97	0.95	0.91	4	-
GCF_900155425.1	s__Parabacteroides massiliensis	88.3538	995	1467	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.33	99.33	0.93	0.93	2	-
GCA_900760525.1	s__Parabacteroides sp900760525	87.3746	913	1467	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.93	98.92	0.84	0.82	3	-
GCA_910577325.1	s__Parabacteroides sp910577325	86.9961	857	1467	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017937385.1	s__Parabacteroides sp017937385	84.2533	774	1467	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000969825.1	s__Parabacteroides gordonii	79.0775	495	1467	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.64	96.69	0.92	0.81	6	-
--------------------------------------------------------------------------------
[2024-01-24 14:14:52,259] [INFO] GTDB search result was written to GCF_900445495.1_52683_B04_genomic.fna/result_gtdb.tsv
[2024-01-24 14:14:52,260] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:14:52,264] [INFO] DFAST_QC result json was written to GCF_900445495.1_52683_B04_genomic.fna/dqc_result.json
[2024-01-24 14:14:52,264] [INFO] DFAST_QC completed!
[2024-01-24 14:14:52,264] [INFO] Total running time: 0h1m51s