[2024-01-24 11:05:03,930] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:03,942] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:03,942] [INFO] DQC Reference Directory: /var/lib/cwl/stg3ca89768-3908-4c0d-b276-d2287eee5e09/dqc_reference
[2024-01-24 11:05:05,764] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:05,766] [INFO] Task started: Prodigal
[2024-01-24 11:05:05,767] [INFO] Running command: gunzip -c /var/lib/cwl/stg9302b455-19ec-4ffa-9b99-720a1587631d/GCF_024330105.1_ASM2433010v1_genomic.fna.gz | prodigal -d GCF_024330105.1_ASM2433010v1_genomic.fna/cds.fna -a GCF_024330105.1_ASM2433010v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:17,018] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:17,018] [INFO] Task started: HMMsearch
[2024-01-24 11:05:17,019] [INFO] Running command: hmmsearch --tblout GCF_024330105.1_ASM2433010v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3ca89768-3908-4c0d-b276-d2287eee5e09/dqc_reference/reference_markers.hmm GCF_024330105.1_ASM2433010v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:17,298] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:17,299] [INFO] Found 6/6 markers.
[2024-01-24 11:05:17,333] [INFO] Query marker FASTA was written to GCF_024330105.1_ASM2433010v1_genomic.fna/markers.fasta
[2024-01-24 11:05:17,333] [INFO] Task started: Blastn
[2024-01-24 11:05:17,333] [INFO] Running command: blastn -query GCF_024330105.1_ASM2433010v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ca89768-3908-4c0d-b276-d2287eee5e09/dqc_reference/reference_markers.fasta -out GCF_024330105.1_ASM2433010v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:17,911] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:17,913] [INFO] Selected 25 target genomes.
[2024-01-24 11:05:17,914] [INFO] Target genome list was writen to GCF_024330105.1_ASM2433010v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:17,936] [INFO] Task started: fastANI
[2024-01-24 11:05:17,936] [INFO] Running command: fastANI --query /var/lib/cwl/stg9302b455-19ec-4ffa-9b99-720a1587631d/GCF_024330105.1_ASM2433010v1_genomic.fna.gz --refList GCF_024330105.1_ASM2433010v1_genomic.fna/target_genomes.txt --output GCF_024330105.1_ASM2433010v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:36,388] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:36,389] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3ca89768-3908-4c0d-b276-d2287eee5e09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:36,389] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3ca89768-3908-4c0d-b276-d2287eee5e09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:36,395] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:05:36,395] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:05:36,396] [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 johnsonii	strain=DSM 18315	GCA_025151045.1	387661	387661	type	True	78.2201	54	1092	95	below_threshold
Parabacteroides johnsonii	strain=DSM 18315	GCA_000156495.1	387661	387661	type	True	78.0978	52	1092	95	below_threshold
Coprobacter secundus subsp. similis	strain=2CBH44	GCA_015097275.1	2751153	1501392	type	True	77.5815	173	1092	95	below_threshold
Bacteroides nordii	strain=FDAARGOS_1461	GCA_019930665.1	291645	291645	type	True	77.4702	59	1092	95	below_threshold
Coprobacter fastidiosus	strain=NSB1	GCA_000473955.1	1099853	1099853	type	True	77.321	158	1092	95	below_threshold
Coprobacter fastidiosus	strain=NSB1	GCA_003634345.1	1099853	1099853	type	True	77.3102	162	1092	95	below_threshold
Barnesiella intestinihominis	strain=YIT 11860	GCA_000296465.1	487174	487174	type	True	77.0309	70	1092	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:36,397] [INFO] DFAST Taxonomy check result was written to GCF_024330105.1_ASM2433010v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:36,397] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:36,397] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:36,398] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3ca89768-3908-4c0d-b276-d2287eee5e09/dqc_reference/checkm_data
[2024-01-24 11:05:36,398] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:36,432] [INFO] Task started: CheckM
[2024-01-24 11:05:36,432] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024330105.1_ASM2433010v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024330105.1_ASM2433010v1_genomic.fna/checkm_input GCF_024330105.1_ASM2433010v1_genomic.fna/checkm_result
[2024-01-24 11:06:09,243] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:09,244] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:09,258] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:09,258] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:09,259] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024330105.1_ASM2433010v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:09,259] [INFO] Task started: Blastn
[2024-01-24 11:06:09,259] [INFO] Running command: blastn -query GCF_024330105.1_ASM2433010v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ca89768-3908-4c0d-b276-d2287eee5e09/dqc_reference/reference_markers_gtdb.fasta -out GCF_024330105.1_ASM2433010v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:10,099] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:10,102] [INFO] Selected 33 target genomes.
[2024-01-24 11:06:10,102] [INFO] Target genome list was writen to GCF_024330105.1_ASM2433010v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:10,120] [INFO] Task started: fastANI
[2024-01-24 11:06:10,121] [INFO] Running command: fastANI --query /var/lib/cwl/stg9302b455-19ec-4ffa-9b99-720a1587631d/GCF_024330105.1_ASM2433010v1_genomic.fna.gz --refList GCF_024330105.1_ASM2433010v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024330105.1_ASM2433010v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:27,544] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:27,550] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:06:27,550] [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_000156495.1	s__Parabacteroides johnsonii	78.1895	50	1092	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.42	96.67	0.88	0.77	13	-
GCA_902363425.1	s__CABJAA01 sp003150885	77.789	100	1092	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Barnesiellaceae;g__CABJAA01	95.0	99.11	99.10	0.93	0.92	5	-
GCA_000803105.1	s__Coprobacter secundus	77.7298	181	1092	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Coprobacteraceae;g__Coprobacter	95.0	97.96	96.86	0.90	0.85	6	-
GCA_900547555.1	s__UBA11471 sp900547555	77.3444	59	1092	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA11471;g__UBA11471	95.0	98.22	98.22	0.90	0.90	2	-
GCF_003634345.1	s__Coprobacter fastidiosus	77.3136	161	1092	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Coprobacteraceae;g__Coprobacter	95.0	98.46	97.98	0.89	0.59	13	-
GCA_900545915.1	s__Coprobacter sp900545915	77.2429	153	1092	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Coprobacteraceae;g__Coprobacter	95.0	97.49	96.20	0.84	0.83	3	-
GCA_900538555.1	s__UMGS27 sp900538555	77.168	63	1092	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Barnesiellaceae;g__UMGS27	95.0	99.31	98.62	0.96	0.93	3	-
GCA_000434215.1	s__UBA11471 sp000434215	77.0159	61	1092	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA11471;g__UBA11471	95.0	99.32	98.64	0.92	0.84	6	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:27,551] [INFO] GTDB search result was written to GCF_024330105.1_ASM2433010v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:27,552] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:27,554] [INFO] DFAST_QC result json was written to GCF_024330105.1_ASM2433010v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:27,554] [INFO] DFAST_QC completed!
[2024-01-24 11:06:27,554] [INFO] Total running time: 0h1m24s