[2024-01-25 17:45:35,794] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:45:35,795] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:45:35,795] [INFO] DQC Reference Directory: /var/lib/cwl/stg130ce8e0-974d-4a5f-aa41-2a1115047595/dqc_reference
[2024-01-25 17:45:36,950] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:45:36,952] [INFO] Task started: Prodigal
[2024-01-25 17:45:36,952] [INFO] Running command: gunzip -c /var/lib/cwl/stg4d24516a-5eed-4a94-b613-13fcb628240e/GCF_020567425.1_ASM2056742v1_genomic.fna.gz | prodigal -d GCF_020567425.1_ASM2056742v1_genomic.fna/cds.fna -a GCF_020567425.1_ASM2056742v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:45:54,109] [INFO] Task succeeded: Prodigal
[2024-01-25 17:45:54,109] [INFO] Task started: HMMsearch
[2024-01-25 17:45:54,110] [INFO] Running command: hmmsearch --tblout GCF_020567425.1_ASM2056742v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg130ce8e0-974d-4a5f-aa41-2a1115047595/dqc_reference/reference_markers.hmm GCF_020567425.1_ASM2056742v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:45:54,312] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:45:54,313] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg4d24516a-5eed-4a94-b613-13fcb628240e/GCF_020567425.1_ASM2056742v1_genomic.fna.gz]
[2024-01-25 17:45:54,344] [INFO] Query marker FASTA was written to GCF_020567425.1_ASM2056742v1_genomic.fna/markers.fasta
[2024-01-25 17:45:54,345] [INFO] Task started: Blastn
[2024-01-25 17:45:54,345] [INFO] Running command: blastn -query GCF_020567425.1_ASM2056742v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg130ce8e0-974d-4a5f-aa41-2a1115047595/dqc_reference/reference_markers.fasta -out GCF_020567425.1_ASM2056742v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:45:54,853] [INFO] Task succeeded: Blastn
[2024-01-25 17:45:54,857] [INFO] Selected 14 target genomes.
[2024-01-25 17:45:54,857] [INFO] Target genome list was writen to GCF_020567425.1_ASM2056742v1_genomic.fna/target_genomes.txt
[2024-01-25 17:45:54,868] [INFO] Task started: fastANI
[2024-01-25 17:45:54,868] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d24516a-5eed-4a94-b613-13fcb628240e/GCF_020567425.1_ASM2056742v1_genomic.fna.gz --refList GCF_020567425.1_ASM2056742v1_genomic.fna/target_genomes.txt --output GCF_020567425.1_ASM2056742v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:46:07,605] [INFO] Task succeeded: fastANI
[2024-01-25 17:46:07,605] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg130ce8e0-974d-4a5f-aa41-2a1115047595/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:46:07,606] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg130ce8e0-974d-4a5f-aa41-2a1115047595/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:46:07,616] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:46:07,616] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:46:07,616] [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
Haloprofundus halophilus	strain=NK23	GCA_003439925.1	2283527	2283527	type	True	78.9599	527	1349	95	below_threshold
Halogeometricum rufum	strain=CGMCC 1.7736	GCA_900112175.1	553469	553469	type	True	78.8051	560	1349	95	below_threshold
Haloferax sulfurifontis	strain=ATCC BAA-897	GCA_000337835.1	255616	255616	type	True	78.7403	537	1349	95	below_threshold
Haloferax volcanii	strain=DS2	GCA_000337315.1	2246	2246	type	True	78.7197	524	1349	95	below_threshold
Halegenticoccus tardaugens	strain=SYSU A00711	GCA_004116405.1	2071624	2071624	type	True	78.7041	513	1349	95	below_threshold
Haloferax volcanii	strain=DS2	GCA_000025685.1	2246	2246	type	True	78.6583	538	1349	95	below_threshold
Haloferax sulfurifontis	strain=CCM 7217	GCA_014635105.1	255616	255616	type	True	78.5724	552	1349	95	below_threshold
Halostella salina	strain=CBA1114	GCA_003675855.1	1547897	1547897	type	True	78.3523	480	1349	95	below_threshold
Halorussus rarus	strain=TBN4	GCA_003369835.1	660515	660515	type	True	77.9783	478	1349	95	below_threshold
Haloarchaeobius litoreus	strain=GX1	GCA_024495425.1	755306	755306	type	True	77.9612	448	1349	95	below_threshold
Halorientalis litorea	strain=ZY14	GCA_023028225.1	2931977	2931977	type	True	77.937	364	1349	95	below_threshold
Halorussus halobius	strain=HD8-83	GCA_004765805.1	1710537	1710537	type	True	77.8503	472	1349	95	below_threshold
Natronoarchaeum rubrum	strain=GX48	GCA_024494695.1	755311	755311	type	True	77.4996	437	1349	95	below_threshold
Halorientalis brevis	strain=YC89	GCA_023077655.1	1126241	1126241	type	True	77.4398	339	1349	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:46:07,617] [INFO] DFAST Taxonomy check result was written to GCF_020567425.1_ASM2056742v1_genomic.fna/tc_result.tsv
[2024-01-25 17:46:07,617] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:46:07,618] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:46:07,618] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg130ce8e0-974d-4a5f-aa41-2a1115047595/dqc_reference/checkm_data
[2024-01-25 17:46:07,618] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:46:07,660] [INFO] Task started: CheckM
[2024-01-25 17:46:07,660] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020567425.1_ASM2056742v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020567425.1_ASM2056742v1_genomic.fna/checkm_input GCF_020567425.1_ASM2056742v1_genomic.fna/checkm_result
[2024-01-25 17:46:54,944] [INFO] Task succeeded: CheckM
[2024-01-25 17:46:54,945] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:46:54,962] [INFO] ===== Completeness check finished =====
[2024-01-25 17:46:54,962] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:46:54,963] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020567425.1_ASM2056742v1_genomic.fna/markers.fasta)
[2024-01-25 17:46:54,963] [INFO] Task started: Blastn
[2024-01-25 17:46:54,963] [INFO] Running command: blastn -query GCF_020567425.1_ASM2056742v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg130ce8e0-974d-4a5f-aa41-2a1115047595/dqc_reference/reference_markers_gtdb.fasta -out GCF_020567425.1_ASM2056742v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:46:55,573] [INFO] Task succeeded: Blastn
[2024-01-25 17:46:55,576] [INFO] Selected 15 target genomes.
[2024-01-25 17:46:55,576] [INFO] Target genome list was writen to GCF_020567425.1_ASM2056742v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:46:55,590] [INFO] Task started: fastANI
[2024-01-25 17:46:55,590] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d24516a-5eed-4a94-b613-13fcb628240e/GCF_020567425.1_ASM2056742v1_genomic.fna.gz --refList GCF_020567425.1_ASM2056742v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020567425.1_ASM2056742v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:47:07,741] [INFO] Task succeeded: fastANI
[2024-01-25 17:47:07,751] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 17:47:07,751] [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_003439925.1	s__Haloprofundus halophilus	78.9351	531	1349	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloprofundus	95.0	98.76	98.76	0.93	0.93	2	-
GCF_900112175.1	s__Halogeometricum rufum	78.8323	555	1349	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halogeometricum	95.0	98.26	98.26	0.87	0.87	2	-
GCF_000337835.1	s__Haloferax sulfurifontis	78.7573	535	1349	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	96.9285	99.04	99.04	0.92	0.92	2	-
GCF_000336775.1	s__Haloferax gibbonsii	78.7493	563	1349	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	96.8304	98.89	98.78	0.89	0.88	5	-
GCF_000337795.1	s__Haloferax denitrificans	78.7047	565	1349	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	96.9285	N/A	N/A	N/A	N/A	1	-
GCF_000025685.1	s__Haloferax volcanii	78.6782	534	1349	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	95.0	98.27	96.62	0.93	0.89	21	-
GCA_004116405.1	s__Halegenticoccus sp004116405	78.6779	517	1349	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halegenticoccus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003342675.1	s__Haloplanus rubicundus	78.5149	458	1349	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloplanus	95.0	98.71	98.71	0.88	0.88	2	-
GCF_009762275.1	s__Haloplanus rallus	78.4733	424	1349	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloplanus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003675875.1	s__Halostella sp003675875	78.0436	502	1349	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__QS-9-68-17;g__Halostella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003369835.1	s__Halorussus rarus	77.9735	478	1349	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Halorussus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001261915.1	s__Halorubrum sp001261915	77.8929	370	1349	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004765805.1	s__Halorussus sp004765805	77.847	470	1349	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Halorussus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013391635.1	s__Natronomonas gomsonensis	77.4243	368	1349	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003021325.1	s__Natronomonas sp003021325	76.6437	218	1349	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:47:07,752] [INFO] GTDB search result was written to GCF_020567425.1_ASM2056742v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:47:07,753] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:47:07,756] [INFO] DFAST_QC result json was written to GCF_020567425.1_ASM2056742v1_genomic.fna/dqc_result.json
[2024-01-25 17:47:07,756] [INFO] DFAST_QC completed!
[2024-01-25 17:47:07,756] [INFO] Total running time: 0h1m32s