[2024-01-24 14:05:49,179] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:49,181] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:49,181] [INFO] DQC Reference Directory: /var/lib/cwl/stg94fbc307-0c7b-4023-b270-4cbf049a22f0/dqc_reference
[2024-01-24 14:05:50,512] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:50,512] [INFO] Task started: Prodigal
[2024-01-24 14:05:50,513] [INFO] Running command: gunzip -c /var/lib/cwl/stgf3ce2ced-9e1b-41a7-be44-ffdd792018ae/GCF_014287545.1_ASM1428754v1_genomic.fna.gz | prodigal -d GCF_014287545.1_ASM1428754v1_genomic.fna/cds.fna -a GCF_014287545.1_ASM1428754v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:24,238] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:24,239] [INFO] Task started: HMMsearch
[2024-01-24 14:06:24,239] [INFO] Running command: hmmsearch --tblout GCF_014287545.1_ASM1428754v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg94fbc307-0c7b-4023-b270-4cbf049a22f0/dqc_reference/reference_markers.hmm GCF_014287545.1_ASM1428754v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:24,656] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:24,658] [INFO] Found 6/6 markers.
[2024-01-24 14:06:24,717] [INFO] Query marker FASTA was written to GCF_014287545.1_ASM1428754v1_genomic.fna/markers.fasta
[2024-01-24 14:06:24,718] [INFO] Task started: Blastn
[2024-01-24 14:06:24,718] [INFO] Running command: blastn -query GCF_014287545.1_ASM1428754v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg94fbc307-0c7b-4023-b270-4cbf049a22f0/dqc_reference/reference_markers.fasta -out GCF_014287545.1_ASM1428754v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:25,442] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:25,446] [INFO] Selected 11 target genomes.
[2024-01-24 14:06:25,447] [INFO] Target genome list was writen to GCF_014287545.1_ASM1428754v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:25,452] [INFO] Task started: fastANI
[2024-01-24 14:06:25,452] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3ce2ced-9e1b-41a7-be44-ffdd792018ae/GCF_014287545.1_ASM1428754v1_genomic.fna.gz --refList GCF_014287545.1_ASM1428754v1_genomic.fna/target_genomes.txt --output GCF_014287545.1_ASM1428754v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:39,296] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:39,296] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg94fbc307-0c7b-4023-b270-4cbf049a22f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:39,296] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg94fbc307-0c7b-4023-b270-4cbf049a22f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:39,306] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:39,306] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:39,306] [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 goldsteinii	strain=DSM 19448	GCA_000969835.1	328812	328812	type	True	95.3104	1691	2376	95	conclusive
Parabacteroides faecis	strain=DSM 102983	GCA_014199665.1	1217282	1217282	type	True	84.3395	1472	2376	95	below_threshold
Parabacteroides faecis	strain=JCM 18682	GCA_014647375.1	1217282	1217282	type	True	84.2887	1470	2376	95	below_threshold
Parabacteroides gordonii	strain=DSM 23371	GCA_000428565.1	574930	574930	type	True	83.4548	1228	2376	95	below_threshold
Parabacteroides gordonii	strain=MS-1	GCA_000969825.1	574930	574930	type	True	83.4373	1248	2376	95	below_threshold
Parabacteroides gordonii	strain=FDAARGOS_1522	GCA_020297465.1	574930	574930	type	True	83.4318	1236	2376	95	below_threshold
Parabacteroides timonensis	strain=Marseille-P3236	GCA_900128505.1	1871013	1871013	type	True	82.3127	1151	2376	95	below_threshold
Parabacteroides johnsonii	strain=DSM 18315	GCA_025151045.1	387661	387661	type	True	79.0527	516	2376	95	below_threshold
Parabacteroides merdae	strain=ATCC 43184	GCA_025151215.1	46503	46503	type	True	78.9567	510	2376	95	below_threshold
Bacteroides nordii	strain=FDAARGOS_1461	GCA_019930665.1	291645	291645	type	True	77.6353	101	2376	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:39,308] [INFO] DFAST Taxonomy check result was written to GCF_014287545.1_ASM1428754v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:39,309] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:39,309] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:39,309] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg94fbc307-0c7b-4023-b270-4cbf049a22f0/dqc_reference/checkm_data
[2024-01-24 14:06:39,310] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:39,378] [INFO] Task started: CheckM
[2024-01-24 14:06:39,378] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014287545.1_ASM1428754v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014287545.1_ASM1428754v1_genomic.fna/checkm_input GCF_014287545.1_ASM1428754v1_genomic.fna/checkm_result
[2024-01-24 14:08:09,182] [INFO] Task succeeded: CheckM
[2024-01-24 14:08:09,183] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:08:09,202] [INFO] ===== Completeness check finished =====
[2024-01-24 14:08:09,203] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:08:09,203] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014287545.1_ASM1428754v1_genomic.fna/markers.fasta)
[2024-01-24 14:08:09,204] [INFO] Task started: Blastn
[2024-01-24 14:08:09,204] [INFO] Running command: blastn -query GCF_014287545.1_ASM1428754v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg94fbc307-0c7b-4023-b270-4cbf049a22f0/dqc_reference/reference_markers_gtdb.fasta -out GCF_014287545.1_ASM1428754v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:08:10,083] [INFO] Task succeeded: Blastn
[2024-01-24 14:08:10,087] [INFO] Selected 9 target genomes.
[2024-01-24 14:08:10,087] [INFO] Target genome list was writen to GCF_014287545.1_ASM1428754v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:08:10,093] [INFO] Task started: fastANI
[2024-01-24 14:08:10,093] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3ce2ced-9e1b-41a7-be44-ffdd792018ae/GCF_014287545.1_ASM1428754v1_genomic.fna.gz --refList GCF_014287545.1_ASM1428754v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014287545.1_ASM1428754v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:08:22,488] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:22,496] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:08:22,496] [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_000969835.1	s__Parabacteroides goldsteinii	95.3131	1690	2376	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.03	95.33	0.85	0.78	37	conclusive
GCF_014647375.1	s__Parabacteroides faecis	84.3063	1467	2376	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.52	97.91	0.91	0.84	9	-
GCF_003480915.1	s__Parabacteroides sp003480915	83.4943	1243	2376	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.39	97.67	0.93	0.87	5	-
GCF_000969825.1	s__Parabacteroides gordonii	83.432	1249	2376	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.64	96.69	0.92	0.81	6	-
GCF_015550595.1	s__Parabacteroides sp900540715	82.6976	1167	2376	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.96	99.96	0.98	0.97	3	-
GCA_905196875.1	s__Parabacteroides sp905196875	82.5692	1077	2376	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900128505.1	s__Parabacteroides timonensis	82.315	1151	2376	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	97.14	96.11	0.85	0.79	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:08:22,497] [INFO] GTDB search result was written to GCF_014287545.1_ASM1428754v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:08:22,498] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:08:22,501] [INFO] DFAST_QC result json was written to GCF_014287545.1_ASM1428754v1_genomic.fna/dqc_result.json
[2024-01-24 14:08:22,501] [INFO] DFAST_QC completed!
[2024-01-24 14:08:22,501] [INFO] Total running time: 0h2m33s