[2024-01-24 13:28:13,311] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:13,315] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:13,315] [INFO] DQC Reference Directory: /var/lib/cwl/stgdb97a7e9-44a6-4ef9-8a62-ce3ad23de844/dqc_reference
[2024-01-24 13:28:14,645] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:14,646] [INFO] Task started: Prodigal
[2024-01-24 13:28:14,647] [INFO] Running command: gunzip -c /var/lib/cwl/stgf18c3343-01b7-438b-8606-127d7c34af63/GCF_020405185.1_ASM2040518v1_genomic.fna.gz | prodigal -d GCF_020405185.1_ASM2040518v1_genomic.fna/cds.fna -a GCF_020405185.1_ASM2040518v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:32,409] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:32,409] [INFO] Task started: HMMsearch
[2024-01-24 13:28:32,409] [INFO] Running command: hmmsearch --tblout GCF_020405185.1_ASM2040518v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdb97a7e9-44a6-4ef9-8a62-ce3ad23de844/dqc_reference/reference_markers.hmm GCF_020405185.1_ASM2040518v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:32,684] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:32,685] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgf18c3343-01b7-438b-8606-127d7c34af63/GCF_020405185.1_ASM2040518v1_genomic.fna.gz]
[2024-01-24 13:28:32,719] [INFO] Query marker FASTA was written to GCF_020405185.1_ASM2040518v1_genomic.fna/markers.fasta
[2024-01-24 13:28:32,720] [INFO] Task started: Blastn
[2024-01-24 13:28:32,720] [INFO] Running command: blastn -query GCF_020405185.1_ASM2040518v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb97a7e9-44a6-4ef9-8a62-ce3ad23de844/dqc_reference/reference_markers.fasta -out GCF_020405185.1_ASM2040518v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:33,308] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:33,312] [INFO] Selected 11 target genomes.
[2024-01-24 13:28:33,312] [INFO] Target genome list was writen to GCF_020405185.1_ASM2040518v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:33,336] [INFO] Task started: fastANI
[2024-01-24 13:28:33,337] [INFO] Running command: fastANI --query /var/lib/cwl/stgf18c3343-01b7-438b-8606-127d7c34af63/GCF_020405185.1_ASM2040518v1_genomic.fna.gz --refList GCF_020405185.1_ASM2040518v1_genomic.fna/target_genomes.txt --output GCF_020405185.1_ASM2040518v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:44,984] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:44,984] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdb97a7e9-44a6-4ef9-8a62-ce3ad23de844/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:44,985] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdb97a7e9-44a6-4ef9-8a62-ce3ad23de844/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:44,997] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:28:44,997] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:28:44,997] [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
Halomicrobium zhouii	strain=CGMCC 1.10457	GCA_900114435.1	767519	767519	type	True	80.7635	709	1280	95	below_threshold
Halomicroarcula salina	strain=JCM 18369	GCA_019061225.1	1429914	1429914	type	True	80.2205	600	1280	95	below_threshold
Halomicroarcula salina	strain=YGHS18	GCA_010119195.1	1429914	1429914	type	True	80.1872	607	1280	95	below_threshold
Halomicroarcula limicola	strain=YGHS32	GCA_010119205.1	1429915	1429915	type	True	79.9835	637	1280	95	below_threshold
Halomicroarcula rubra	strain=F13	GCA_019599465.1	2487747	2487747	type	True	79.6566	605	1280	95	below_threshold
Halosimplex rubrum	strain=R27	GCA_013415885.1	869889	869889	type	True	79.5958	667	1280	95	below_threshold
Halostella limicola	strain=LT12	GCA_003675875.1	2448456	2448456	type	True	78.827	557	1280	95	below_threshold
Salinirussus salinus	strain=YGH44	GCA_009831455.1	1198300	1198300	type	True	78.8122	456	1280	95	below_threshold
Halorientalis regularis	strain=TNN28	GCA_023698535.1	660518	660518	type	True	78.7981	507	1280	95	below_threshold
Halorientalis pallida	strain=F13-25	GCA_004118325.1	2479928	2479928	type	True	78.7457	480	1280	95	below_threshold
Halostella litorea	strain=DLLS-108	GCA_004785955.1	2528831	2528831	type	True	78.6563	535	1280	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:45,000] [INFO] DFAST Taxonomy check result was written to GCF_020405185.1_ASM2040518v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:45,001] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:45,001] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:45,001] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdb97a7e9-44a6-4ef9-8a62-ce3ad23de844/dqc_reference/checkm_data
[2024-01-24 13:28:45,003] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:45,047] [INFO] Task started: CheckM
[2024-01-24 13:28:45,047] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020405185.1_ASM2040518v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020405185.1_ASM2040518v1_genomic.fna/checkm_input GCF_020405185.1_ASM2040518v1_genomic.fna/checkm_result
[2024-01-24 13:29:33,390] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:33,392] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 5.56%
Strain heterogeneity: 25.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:33,415] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:33,415] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:33,416] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020405185.1_ASM2040518v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:33,416] [INFO] Task started: Blastn
[2024-01-24 13:29:33,416] [INFO] Running command: blastn -query GCF_020405185.1_ASM2040518v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb97a7e9-44a6-4ef9-8a62-ce3ad23de844/dqc_reference/reference_markers_gtdb.fasta -out GCF_020405185.1_ASM2040518v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:33,984] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:33,988] [INFO] Selected 11 target genomes.
[2024-01-24 13:29:33,989] [INFO] Target genome list was writen to GCF_020405185.1_ASM2040518v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:33,997] [INFO] Task started: fastANI
[2024-01-24 13:29:33,997] [INFO] Running command: fastANI --query /var/lib/cwl/stgf18c3343-01b7-438b-8606-127d7c34af63/GCF_020405185.1_ASM2040518v1_genomic.fna.gz --refList GCF_020405185.1_ASM2040518v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020405185.1_ASM2040518v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:43,456] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:43,473] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:29:43,473] [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_900114435.1	s__Halomicrobium zhouii	80.7392	711	1280	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010119195.1	s__Haloarcula salina	80.1881	608	1280	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010119205.1	s__Halomicroarcula limicola	80.049	629	1280	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halomicroarcula	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014647235.1	s__Halomicroarcula pellucida	79.4686	568	1280	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halomicroarcula	95.0	96.63	96.63	0.87	0.87	2	-
GCF_002844335.1	s__Haloarcula taiwanensis	79.3869	456	1280	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.0	99.00	98.44	0.94	0.92	4	-
GCA_003021655.1	s__QS-4-69-31 sp003021655	78.9691	461	1280	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__QS-4-69-31	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003675875.1	s__Halostella sp003675875	78.8422	554	1280	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_004118325.1	s__Halorientalis sp004118325	78.7451	480	1280	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halorientalis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003675855.1	s__Halostella salina	78.7291	513	1280	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__QS-9-68-17;g__Halostella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004785955.1	s__Halostella litorea	78.7257	526	1280	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__QS-9-68-17;g__Halostella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003021305.1	s__QH-10-67-22 sp003021305	78.4762	405	1280	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__QH-10-67-22	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:43,475] [INFO] GTDB search result was written to GCF_020405185.1_ASM2040518v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:43,475] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:43,479] [INFO] DFAST_QC result json was written to GCF_020405185.1_ASM2040518v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:43,479] [INFO] DFAST_QC completed!
[2024-01-24 13:29:43,479] [INFO] Total running time: 0h1m30s