[2024-01-24 15:02:24,236] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:24,239] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:24,240] [INFO] DQC Reference Directory: /var/lib/cwl/stg155b3aee-2626-41cf-a529-8af46726b370/dqc_reference
[2024-01-24 15:02:26,427] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:26,428] [INFO] Task started: Prodigal
[2024-01-24 15:02:26,428] [INFO] Running command: gunzip -c /var/lib/cwl/stg0d2a8923-6ddc-4d05-b51f-4649c5a058a9/GCF_017874235.1_ASM1787423v1_genomic.fna.gz | prodigal -d GCF_017874235.1_ASM1787423v1_genomic.fna/cds.fna -a GCF_017874235.1_ASM1787423v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:40,655] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:40,656] [INFO] Task started: HMMsearch
[2024-01-24 15:02:40,656] [INFO] Running command: hmmsearch --tblout GCF_017874235.1_ASM1787423v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg155b3aee-2626-41cf-a529-8af46726b370/dqc_reference/reference_markers.hmm GCF_017874235.1_ASM1787423v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:40,916] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:40,917] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg0d2a8923-6ddc-4d05-b51f-4649c5a058a9/GCF_017874235.1_ASM1787423v1_genomic.fna.gz]
[2024-01-24 15:02:40,946] [INFO] Query marker FASTA was written to GCF_017874235.1_ASM1787423v1_genomic.fna/markers.fasta
[2024-01-24 15:02:40,946] [INFO] Task started: Blastn
[2024-01-24 15:02:40,946] [INFO] Running command: blastn -query GCF_017874235.1_ASM1787423v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg155b3aee-2626-41cf-a529-8af46726b370/dqc_reference/reference_markers.fasta -out GCF_017874235.1_ASM1787423v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:41,616] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:41,622] [INFO] Selected 7 target genomes.
[2024-01-24 15:02:41,623] [INFO] Target genome list was writen to GCF_017874235.1_ASM1787423v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:41,638] [INFO] Task started: fastANI
[2024-01-24 15:02:41,638] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d2a8923-6ddc-4d05-b51f-4649c5a058a9/GCF_017874235.1_ASM1787423v1_genomic.fna.gz --refList GCF_017874235.1_ASM1787423v1_genomic.fna/target_genomes.txt --output GCF_017874235.1_ASM1787423v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:02:48,080] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:48,080] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg155b3aee-2626-41cf-a529-8af46726b370/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:02:48,081] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg155b3aee-2626-41cf-a529-8af46726b370/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:02:48,088] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:02:48,089] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:02:48,089] [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
Halolamina salifodinae	strain=DSM 26232	GCA_017874235.1	1202767	1202767	type	True	100.0	910	911	95	conclusive
Halolamina pelagica	strain=CGMCC 1.10329	GCA_900115675.1	699431	699431	type	True	86.0761	670	911	95	below_threshold
Halolamina rubra	strain=CBA1107	GCA_000739555.1	1380430	1380430	type	True	85.8827	648	911	95	below_threshold
Halolamina sediminis	strain=halo7	GCA_001282785.1	1480675	1480675	type	True	85.2057	673	911	95	below_threshold
Halorubrum rutilum	strain=YJ-18-S1	GCA_024494565.1	1364933	1364933	type	True	78.1543	361	911	95	below_threshold
Halobaculum gomorrense	strain=DSM 9297	GCA_900129775.1	43928	43928	type	True	78.1182	388	911	95	below_threshold
Halalkaliarchaeum desulfuricum	strain=AArc-Sl	GCA_002952775.1	2055893	2055893	type	True	77.4521	231	911	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:02:48,090] [INFO] DFAST Taxonomy check result was written to GCF_017874235.1_ASM1787423v1_genomic.fna/tc_result.tsv
[2024-01-24 15:02:48,091] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:02:48,091] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:02:48,091] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg155b3aee-2626-41cf-a529-8af46726b370/dqc_reference/checkm_data
[2024-01-24 15:02:48,093] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:02:48,125] [INFO] Task started: CheckM
[2024-01-24 15:02:48,125] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017874235.1_ASM1787423v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017874235.1_ASM1787423v1_genomic.fna/checkm_input GCF_017874235.1_ASM1787423v1_genomic.fna/checkm_result
[2024-01-24 15:03:29,343] [INFO] Task succeeded: CheckM
[2024-01-24 15:03:29,344] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:03:29,380] [INFO] ===== Completeness check finished =====
[2024-01-24 15:03:29,381] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:03:29,381] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017874235.1_ASM1787423v1_genomic.fna/markers.fasta)
[2024-01-24 15:03:29,381] [INFO] Task started: Blastn
[2024-01-24 15:03:29,381] [INFO] Running command: blastn -query GCF_017874235.1_ASM1787423v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg155b3aee-2626-41cf-a529-8af46726b370/dqc_reference/reference_markers_gtdb.fasta -out GCF_017874235.1_ASM1787423v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:29,919] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:29,922] [INFO] Selected 6 target genomes.
[2024-01-24 15:03:29,922] [INFO] Target genome list was writen to GCF_017874235.1_ASM1787423v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:03:29,931] [INFO] Task started: fastANI
[2024-01-24 15:03:29,932] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d2a8923-6ddc-4d05-b51f-4649c5a058a9/GCF_017874235.1_ASM1787423v1_genomic.fna.gz --refList GCF_017874235.1_ASM1787423v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017874235.1_ASM1787423v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:03:36,268] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:36,275] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:03:36,275] [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_017874235.1	s__Halolamina salifodinae	100.0	910	911	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halolamina	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900115675.1	s__Halolamina pelagica	86.0873	668	911	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halolamina	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000739555.1	s__Halolamina rubra	85.8796	648	911	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halolamina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001307315.1	s__Halolamina pelagica_B	85.394	658	911	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halolamina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002025255.2	s__Halolamina sp002025255	85.3679	683	911	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halolamina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001282785.1	s__Halolamina sediminis	85.2049	675	911	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halolamina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:03:36,277] [INFO] GTDB search result was written to GCF_017874235.1_ASM1787423v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:03:36,277] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:03:36,280] [INFO] DFAST_QC result json was written to GCF_017874235.1_ASM1787423v1_genomic.fna/dqc_result.json
[2024-01-24 15:03:36,280] [INFO] DFAST_QC completed!
[2024-01-24 15:03:36,280] [INFO] Total running time: 0h1m12s