[2024-01-25 20:05:35,561] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:05:35,562] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:05:35,562] [INFO] DQC Reference Directory: /var/lib/cwl/stg34133e0f-a0a6-41d2-9134-e92cb50881c5/dqc_reference
[2024-01-25 20:05:36,687] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:05:36,688] [INFO] Task started: Prodigal
[2024-01-25 20:05:36,688] [INFO] Running command: gunzip -c /var/lib/cwl/stgf8b9e534-1e5b-47ec-92c8-36a07e5caa67/GCF_020217425.1_ASM2021742v1_genomic.fna.gz | prodigal -d GCF_020217425.1_ASM2021742v1_genomic.fna/cds.fna -a GCF_020217425.1_ASM2021742v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:05:52,879] [INFO] Task succeeded: Prodigal
[2024-01-25 20:05:52,879] [INFO] Task started: HMMsearch
[2024-01-25 20:05:52,879] [INFO] Running command: hmmsearch --tblout GCF_020217425.1_ASM2021742v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg34133e0f-a0a6-41d2-9134-e92cb50881c5/dqc_reference/reference_markers.hmm GCF_020217425.1_ASM2021742v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:05:53,110] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:05:53,111] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgf8b9e534-1e5b-47ec-92c8-36a07e5caa67/GCF_020217425.1_ASM2021742v1_genomic.fna.gz]
[2024-01-25 20:05:53,145] [INFO] Query marker FASTA was written to GCF_020217425.1_ASM2021742v1_genomic.fna/markers.fasta
[2024-01-25 20:05:53,145] [INFO] Task started: Blastn
[2024-01-25 20:05:53,145] [INFO] Running command: blastn -query GCF_020217425.1_ASM2021742v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34133e0f-a0a6-41d2-9134-e92cb50881c5/dqc_reference/reference_markers.fasta -out GCF_020217425.1_ASM2021742v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:05:53,672] [INFO] Task succeeded: Blastn
[2024-01-25 20:05:53,674] [INFO] Selected 15 target genomes.
[2024-01-25 20:05:53,675] [INFO] Target genome list was writen to GCF_020217425.1_ASM2021742v1_genomic.fna/target_genomes.txt
[2024-01-25 20:05:53,680] [INFO] Task started: fastANI
[2024-01-25 20:05:53,680] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8b9e534-1e5b-47ec-92c8-36a07e5caa67/GCF_020217425.1_ASM2021742v1_genomic.fna.gz --refList GCF_020217425.1_ASM2021742v1_genomic.fna/target_genomes.txt --output GCF_020217425.1_ASM2021742v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:06:07,021] [INFO] Task succeeded: fastANI
[2024-01-25 20:06:07,021] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg34133e0f-a0a6-41d2-9134-e92cb50881c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:06:07,022] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg34133e0f-a0a6-41d2-9134-e92cb50881c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:06:07,031] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:06:07,031] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:06:07,031] [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	80.5496	679	1416	95	below_threshold
Halomicroarcula salina	strain=YGHS18	GCA_010119195.1	1429914	1429914	type	True	80.1781	608	1416	95	below_threshold
Halomicroarcula salina	strain=JCM 18369	GCA_019061225.1	1429914	1429914	type	True	80.1386	613	1416	95	below_threshold
Halomicroarcula limicola	strain=YGHS32	GCA_010119205.1	1429915	1429915	type	True	79.9373	605	1416	95	below_threshold
Halosimplex halophilum	strain=TH32	GCA_004698125.1	2559572	2559572	type	True	79.763	652	1416	95	below_threshold
Halomicroarcula rubra	strain=F13	GCA_019599465.1	2487747	2487747	type	True	79.7433	625	1416	95	below_threshold
Halosimplex rubrum	strain=R27	GCA_013415885.1	869889	869889	type	True	79.6111	662	1416	95	below_threshold
Halosimplex pelagicum	strain=R2	GCA_013415905.1	869886	869886	type	True	79.6074	657	1416	95	below_threshold
Halomicroarcula pellucida	strain=CECT 7537	GCA_019599515.1	1427151	1427151	type	True	79.383	565	1416	95	below_threshold
Halosimplex litoreum	strain=YGH94	GCA_016065055.1	1198301	1198301	type	True	79.3646	601	1416	95	below_threshold
Halomicroarcula pellucida	strain=JCM 17820	GCA_014647235.1	1427151	1427151	type	True	79.3569	579	1416	95	below_threshold
Haloarcula japonica	strain=DSM 6131	GCA_000336635.1	29282	29282	type	True	79.0342	490	1416	95	below_threshold
Halostella limicola	strain=LT12	GCA_003675875.1	2448456	2448456	type	True	78.8966	559	1416	95	below_threshold
Salinirussus salinus	strain=YGH44	GCA_009831455.1	1198300	1198300	type	True	78.7995	438	1416	95	below_threshold
Halostella litorea	strain=DLLS-108	GCA_004785955.1	2528831	2528831	type	True	78.7864	522	1416	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:06:07,033] [INFO] DFAST Taxonomy check result was written to GCF_020217425.1_ASM2021742v1_genomic.fna/tc_result.tsv
[2024-01-25 20:06:07,034] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:06:07,034] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:06:07,034] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg34133e0f-a0a6-41d2-9134-e92cb50881c5/dqc_reference/checkm_data
[2024-01-25 20:06:07,035] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:06:07,092] [INFO] Task started: CheckM
[2024-01-25 20:06:07,092] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020217425.1_ASM2021742v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020217425.1_ASM2021742v1_genomic.fna/checkm_input GCF_020217425.1_ASM2021742v1_genomic.fna/checkm_result
[2024-01-25 20:06:51,178] [INFO] Task succeeded: CheckM
[2024-01-25 20:06:51,179] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 5.56%
Strain heterogeneity: 25.00%
--------------------------------------------------------------------------------
[2024-01-25 20:06:51,195] [INFO] ===== Completeness check finished =====
[2024-01-25 20:06:51,196] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:06:51,196] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020217425.1_ASM2021742v1_genomic.fna/markers.fasta)
[2024-01-25 20:06:51,196] [INFO] Task started: Blastn
[2024-01-25 20:06:51,197] [INFO] Running command: blastn -query GCF_020217425.1_ASM2021742v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34133e0f-a0a6-41d2-9134-e92cb50881c5/dqc_reference/reference_markers_gtdb.fasta -out GCF_020217425.1_ASM2021742v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:06:51,770] [INFO] Task succeeded: Blastn
[2024-01-25 20:06:51,773] [INFO] Selected 14 target genomes.
[2024-01-25 20:06:51,773] [INFO] Target genome list was writen to GCF_020217425.1_ASM2021742v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:06:51,787] [INFO] Task started: fastANI
[2024-01-25 20:06:51,787] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8b9e534-1e5b-47ec-92c8-36a07e5caa67/GCF_020217425.1_ASM2021742v1_genomic.fna.gz --refList GCF_020217425.1_ASM2021742v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020217425.1_ASM2021742v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:07:04,439] [INFO] Task succeeded: fastANI
[2024-01-25 20:07:04,449] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:07:04,449] [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	80.5212	681	1416	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	80.2016	605	1416	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	79.9573	603	1416	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halomicroarcula	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013415905.1	s__Halosimplex pelagicum	79.6312	660	1416	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halosimplex	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013415885.1	s__Halosimplex rubrum	79.6094	664	1416	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halosimplex	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016065055.1	s__Halosimplex litoreum	79.3712	599	1416	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halosimplex	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005406125.1	s__Haloarcula sp005406125	79.3562	510	1416	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647235.1	s__Halomicroarcula pellucida	79.3495	579	1416	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halomicroarcula	95.0	96.63	96.63	0.87	0.87	2	-
GCF_000336635.1	s__Haloarcula japonica	79.0129	491	1416	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001485575.1	s__Haloarcula sp001485575	78.9058	442	1416	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003675875.1	s__Halostella sp003675875	78.897	556	1416	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	-
GCA_003021655.1	s__QS-4-69-31 sp003021655	78.8096	434	1416	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	-
GCA_003023565.1	s__Halostella sp003023565	78.479	424	1416	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	78.4114	385	1416	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	-
--------------------------------------------------------------------------------
[2024-01-25 20:07:04,450] [INFO] GTDB search result was written to GCF_020217425.1_ASM2021742v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:07:04,451] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:07:04,454] [INFO] DFAST_QC result json was written to GCF_020217425.1_ASM2021742v1_genomic.fna/dqc_result.json
[2024-01-25 20:07:04,454] [INFO] DFAST_QC completed!
[2024-01-25 20:07:04,454] [INFO] Total running time: 0h1m29s