[2023-06-30 05:30:24,365] [INFO] DFAST_QC pipeline started.
[2023-06-30 05:30:24,367] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 05:30:24,367] [INFO] DQC Reference Directory: /var/lib/cwl/stg2f3e93c6-db72-4b58-87d3-0fc2fbb3f59a/dqc_reference
[2023-06-30 05:30:25,691] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 05:30:25,692] [INFO] Task started: Prodigal
[2023-06-30 05:30:25,692] [INFO] Running command: gunzip -c /var/lib/cwl/stg06c0ac55-2ae7-4a2d-ab99-2aa6f006ea6f/GCA_900756185.1_ERS473366_23_genomic.fna.gz | prodigal -d GCA_900756185.1_ERS473366_23_genomic.fna/cds.fna -a GCA_900756185.1_ERS473366_23_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 05:30:45,527] [INFO] Task succeeded: Prodigal
[2023-06-30 05:30:45,528] [INFO] Task started: HMMsearch
[2023-06-30 05:30:45,528] [INFO] Running command: hmmsearch --tblout GCA_900756185.1_ERS473366_23_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2f3e93c6-db72-4b58-87d3-0fc2fbb3f59a/dqc_reference/reference_markers.hmm GCA_900756185.1_ERS473366_23_genomic.fna/protein.faa > /dev/null
[2023-06-30 05:30:45,809] [INFO] Task succeeded: HMMsearch
[2023-06-30 05:30:45,810] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg06c0ac55-2ae7-4a2d-ab99-2aa6f006ea6f/GCA_900756185.1_ERS473366_23_genomic.fna.gz]
[2023-06-30 05:30:45,845] [INFO] Query marker FASTA was written to GCA_900756185.1_ERS473366_23_genomic.fna/markers.fasta
[2023-06-30 05:30:45,846] [INFO] Task started: Blastn
[2023-06-30 05:30:45,846] [INFO] Running command: blastn -query GCA_900756185.1_ERS473366_23_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f3e93c6-db72-4b58-87d3-0fc2fbb3f59a/dqc_reference/reference_markers.fasta -out GCA_900756185.1_ERS473366_23_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 05:30:46,445] [INFO] Task succeeded: Blastn
[2023-06-30 05:30:46,450] [INFO] Selected 9 target genomes.
[2023-06-30 05:30:46,451] [INFO] Target genome list was writen to GCA_900756185.1_ERS473366_23_genomic.fna/target_genomes.txt
[2023-06-30 05:30:46,452] [INFO] Task started: fastANI
[2023-06-30 05:30:46,452] [INFO] Running command: fastANI --query /var/lib/cwl/stg06c0ac55-2ae7-4a2d-ab99-2aa6f006ea6f/GCA_900756185.1_ERS473366_23_genomic.fna.gz --refList GCA_900756185.1_ERS473366_23_genomic.fna/target_genomes.txt --output GCA_900756185.1_ERS473366_23_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 05:30:54,581] [INFO] Task succeeded: fastANI
[2023-06-30 05:30:54,581] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2f3e93c6-db72-4b58-87d3-0fc2fbb3f59a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 05:30:54,582] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2f3e93c6-db72-4b58-87d3-0fc2fbb3f59a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 05:30:54,591] [INFO] Found 9 fastANI hits (4 hits with ANI > threshold)
[2023-06-30 05:30:54,591] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2023-06-30 05:30:54,591] [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	97.4305	628	1239	95	inconclusive
Parabacteroides merdae	strain=ATCC 43184	GCA_000154105.1	46503	46503	type	True	97.4043	625	1239	95	inconclusive
Parabacteroides merdae	strain=ATCC 43184	GCA_025151215.1	46503	46503	type	True	97.3274	637	1239	95	inconclusive
Bacteroides thetaiotaomicron	strain=VPI 5482	GCA_022453665.1	818	818	type	True	96.3846	506	1239	95	inconclusive
Parabacteroides johnsonii	strain=DSM 18315	GCA_025151045.1	387661	387661	type	True	90.5368	586	1239	95	below_threshold
Parabacteroides johnsonii	strain=DSM 18315	GCA_000156495.1	387661	387661	type	True	90.4056	588	1239	95	below_threshold
Bacteroides caccae	strain=ATCC 43185	GCA_025146315.1	47678	47678	suspected-type	True	81.0841	306	1239	95	below_threshold
Bacteroides stercorirosoris	strain=JCM 17103	GCA_000614165.1	871324	871324	type	True	77.816	168	1239	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_025147325.1	46506	46506	suspected-type	True	77.48	138	1239	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 05:30:54,593] [INFO] DFAST Taxonomy check result was written to GCA_900756185.1_ERS473366_23_genomic.fna/tc_result.tsv
[2023-06-30 05:30:54,593] [INFO] ===== Taxonomy check completed =====
[2023-06-30 05:30:54,593] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 05:30:54,594] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2f3e93c6-db72-4b58-87d3-0fc2fbb3f59a/dqc_reference/checkm_data
[2023-06-30 05:30:54,595] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 05:30:54,637] [INFO] Task started: CheckM
[2023-06-30 05:30:54,638] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_900756185.1_ERS473366_23_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_900756185.1_ERS473366_23_genomic.fna/checkm_input GCA_900756185.1_ERS473366_23_genomic.fna/checkm_result
[2023-06-30 05:31:51,781] [INFO] Task succeeded: CheckM
[2023-06-30 05:31:51,782] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 42.71%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 05:31:51,805] [INFO] ===== Completeness check finished =====
[2023-06-30 05:31:51,805] [INFO] ===== Start GTDB Search =====
[2023-06-30 05:31:51,806] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_900756185.1_ERS473366_23_genomic.fna/markers.fasta)
[2023-06-30 05:31:51,806] [INFO] Task started: Blastn
[2023-06-30 05:31:51,806] [INFO] Running command: blastn -query GCA_900756185.1_ERS473366_23_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f3e93c6-db72-4b58-87d3-0fc2fbb3f59a/dqc_reference/reference_markers_gtdb.fasta -out GCA_900756185.1_ERS473366_23_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 05:31:52,586] [INFO] Task succeeded: Blastn
[2023-06-30 05:31:52,590] [INFO] Selected 13 target genomes.
[2023-06-30 05:31:52,590] [INFO] Target genome list was writen to GCA_900756185.1_ERS473366_23_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 05:31:52,592] [INFO] Task started: fastANI
[2023-06-30 05:31:52,592] [INFO] Running command: fastANI --query /var/lib/cwl/stg06c0ac55-2ae7-4a2d-ab99-2aa6f006ea6f/GCA_900756185.1_ERS473366_23_genomic.fna.gz --refList GCA_900756185.1_ERS473366_23_genomic.fna/target_genomes_gtdb.txt --output GCA_900756185.1_ERS473366_23_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 05:32:03,413] [INFO] Task succeeded: fastANI
[2023-06-30 05:32:03,425] [INFO] Found 11 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-30 05:32:03,425] [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	97.4043	625	1239	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.97	97.44	0.89	0.77	85	inconclusive
GCF_000011065.1	s__Bacteroides thetaiotaomicron	96.4835	505	1239	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.45	97.24	0.84	0.75	121	inconclusive
GCF_000156495.1	s__Parabacteroides johnsonii	90.4056	588	1239	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	89.1658	603	1239	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.33	98.97	0.95	0.91	4	-
GCF_900106755.1	s__Bacteroides faecis	88.2728	468	1239	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.27	98.92	0.88	0.84	29	-
GCF_900155425.1	s__Parabacteroides massiliensis	87.8326	562	1239	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	87.0306	503	1239	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	86.7065	472	1239	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900755095.1	s__Bacteroides sp900755095	86.4523	172	1239	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014334015.1	s__Bacteroides intestinigallinarum	83.2816	348	1239	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.71	95.47	0.80	0.53	8	-
GCF_000210075.1	s__Bacteroides xylanisolvens	81.9764	341	1239	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.52	96.81	0.77	0.68	125	-
--------------------------------------------------------------------------------
[2023-06-30 05:32:03,427] [INFO] GTDB search result was written to GCA_900756185.1_ERS473366_23_genomic.fna/result_gtdb.tsv
[2023-06-30 05:32:03,427] [INFO] ===== GTDB Search completed =====
[2023-06-30 05:32:03,430] [INFO] DFAST_QC result json was written to GCA_900756185.1_ERS473366_23_genomic.fna/dqc_result.json
[2023-06-30 05:32:03,430] [INFO] DFAST_QC completed!
[2023-06-30 05:32:03,430] [INFO] Total running time: 0h1m39s