[2024-01-24 11:34:42,932] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:42,933] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:42,933] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f935606-97c8-4166-99da-13efba9f97a7/dqc_reference
[2024-01-24 11:34:44,293] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:44,294] [INFO] Task started: Prodigal
[2024-01-24 11:34:44,294] [INFO] Running command: gunzip -c /var/lib/cwl/stge766a97f-7e6b-41c0-9e8b-61869776a0e7/GCF_022556335.1_ASM2255633v1_genomic.fna.gz | prodigal -d GCF_022556335.1_ASM2255633v1_genomic.fna/cds.fna -a GCF_022556335.1_ASM2255633v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:34:57,140] [INFO] Task succeeded: Prodigal
[2024-01-24 11:34:57,141] [INFO] Task started: HMMsearch
[2024-01-24 11:34:57,141] [INFO] Running command: hmmsearch --tblout GCF_022556335.1_ASM2255633v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f935606-97c8-4166-99da-13efba9f97a7/dqc_reference/reference_markers.hmm GCF_022556335.1_ASM2255633v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:34:57,390] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:34:57,391] [INFO] Found 6/6 markers.
[2024-01-24 11:34:57,413] [INFO] Query marker FASTA was written to GCF_022556335.1_ASM2255633v1_genomic.fna/markers.fasta
[2024-01-24 11:34:57,413] [INFO] Task started: Blastn
[2024-01-24 11:34:57,413] [INFO] Running command: blastn -query GCF_022556335.1_ASM2255633v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f935606-97c8-4166-99da-13efba9f97a7/dqc_reference/reference_markers.fasta -out GCF_022556335.1_ASM2255633v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:34:58,029] [INFO] Task succeeded: Blastn
[2024-01-24 11:34:58,032] [INFO] Selected 9 target genomes.
[2024-01-24 11:34:58,033] [INFO] Target genome list was writen to GCF_022556335.1_ASM2255633v1_genomic.fna/target_genomes.txt
[2024-01-24 11:34:58,039] [INFO] Task started: fastANI
[2024-01-24 11:34:58,039] [INFO] Running command: fastANI --query /var/lib/cwl/stge766a97f-7e6b-41c0-9e8b-61869776a0e7/GCF_022556335.1_ASM2255633v1_genomic.fna.gz --refList GCF_022556335.1_ASM2255633v1_genomic.fna/target_genomes.txt --output GCF_022556335.1_ASM2255633v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:04,626] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:04,626] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f935606-97c8-4166-99da-13efba9f97a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:04,626] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f935606-97c8-4166-99da-13efba9f97a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:04,635] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:35:04,636] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:04,636] [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
Thermus arciformis	strain=JCM 15153	GCA_022556335.1	482827	482827	type	True	100.0	756	760	95	conclusive
Thermus arciformis	strain=CGMCC 1.6992	GCA_900102145.1	482827	482827	type	True	99.9613	752	760	95	conclusive
Thermus thermophilus	strain=HB8	GCA_000091545.1	274	274	type	True	90.9265	566	760	95	below_threshold
Thermus thermophilus	strain=JCM10941	GCA_019973715.1	274	274	type	True	90.9148	574	760	95	below_threshold
Thermus parvatiensis	strain=RL	GCA_001535545.1	456163	456163	type	True	89.9631	543	760	95	below_threshold
Thermus parvatiensis	strain=RL	GCA_000252835.2	456163	456163	type	True	89.7307	538	760	95	below_threshold
Thermus aquaticus	strain=YT-1	GCA_001280255.1	271	271	type	True	86.9589	578	760	95	below_threshold
Thermus igniterrae	strain=ATCC 700962	GCA_000376265.1	88189	88189	type	True	86.9058	588	760	95	below_threshold
Thermus caliditerrae	strain=YIM 77925	GCA_021462525.1	1330700	1330700	type	True	85.8	597	760	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:04,637] [INFO] DFAST Taxonomy check result was written to GCF_022556335.1_ASM2255633v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:04,638] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:04,638] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:04,638] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f935606-97c8-4166-99da-13efba9f97a7/dqc_reference/checkm_data
[2024-01-24 11:35:04,640] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:04,669] [INFO] Task started: CheckM
[2024-01-24 11:35:04,669] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022556335.1_ASM2255633v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022556335.1_ASM2255633v1_genomic.fna/checkm_input GCF_022556335.1_ASM2255633v1_genomic.fna/checkm_result
[2024-01-24 11:35:43,031] [INFO] Task succeeded: CheckM
[2024-01-24 11:35:43,032] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:35:43,048] [INFO] ===== Completeness check finished =====
[2024-01-24 11:35:43,049] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:35:43,049] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022556335.1_ASM2255633v1_genomic.fna/markers.fasta)
[2024-01-24 11:35:43,050] [INFO] Task started: Blastn
[2024-01-24 11:35:43,050] [INFO] Running command: blastn -query GCF_022556335.1_ASM2255633v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f935606-97c8-4166-99da-13efba9f97a7/dqc_reference/reference_markers_gtdb.fasta -out GCF_022556335.1_ASM2255633v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:43,965] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:43,968] [INFO] Selected 14 target genomes.
[2024-01-24 11:35:43,968] [INFO] Target genome list was writen to GCF_022556335.1_ASM2255633v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:35:43,985] [INFO] Task started: fastANI
[2024-01-24 11:35:43,986] [INFO] Running command: fastANI --query /var/lib/cwl/stge766a97f-7e6b-41c0-9e8b-61869776a0e7/GCF_022556335.1_ASM2255633v1_genomic.fna.gz --refList GCF_022556335.1_ASM2255633v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022556335.1_ASM2255633v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:35:53,209] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:53,223] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:35:53,224] [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_900102145.1	s__Thermus arciformis	99.9613	752	760	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002355995.1	s__Thermus thermophilus_C	92.5521	571	760	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.6833	N/A	N/A	N/A	N/A	1	-
GCF_000091545.1	s__Thermus thermophilus	90.9703	564	760	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.7334	98.46	96.78	0.92	0.87	18	-
GCA_001311585.1	s__Thermus sp001311585	90.2348	380	760	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001535545.1	s__Thermus parvatiensis	89.9349	544	760	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.7334	98.79	98.79	0.97	0.97	2	-
GCA_001311545.1	s__Thermus kawarayensis	89.7073	366	760	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647535.1	s__Thermus composti	88.5013	541	760	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000421625.1	s__Thermus islandicus	87.2444	577	760	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001280255.1	s__Thermus aquaticus	86.9798	577	760	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	98.02	97.96	0.92	0.92	3	-
GCF_000794385.1	s__Thermus sp000794385	86.9471	594	760	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000376265.1	s__Thermus igniterrae	86.9055	588	760	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003426945.1	s__Thermus sediminis	86.2996	569	760	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000236585.1	s__Thermus sp000236585	86.0426	581	760	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745065.1	s__Thermus caliditerrae	85.7681	595	760	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:35:53,231] [INFO] GTDB search result was written to GCF_022556335.1_ASM2255633v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:35:53,232] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:35:53,235] [INFO] DFAST_QC result json was written to GCF_022556335.1_ASM2255633v1_genomic.fna/dqc_result.json
[2024-01-24 11:35:53,235] [INFO] DFAST_QC completed!
[2024-01-24 11:35:53,235] [INFO] Total running time: 0h1m10s