[2024-01-25 19:05:50,802] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:05:50,803] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:05:50,804] [INFO] DQC Reference Directory: /var/lib/cwl/stgb522f719-ac45-46a7-af43-2b87ee80cbf9/dqc_reference
[2024-01-25 19:05:51,943] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:05:51,944] [INFO] Task started: Prodigal
[2024-01-25 19:05:51,944] [INFO] Running command: gunzip -c /var/lib/cwl/stg613e98a3-924e-4535-aa28-7a5959e08317/GCF_023074835.1_ASM2307483v1_genomic.fna.gz | prodigal -d GCF_023074835.1_ASM2307483v1_genomic.fna/cds.fna -a GCF_023074835.1_ASM2307483v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:06:10,361] [INFO] Task succeeded: Prodigal
[2024-01-25 19:06:10,361] [INFO] Task started: HMMsearch
[2024-01-25 19:06:10,361] [INFO] Running command: hmmsearch --tblout GCF_023074835.1_ASM2307483v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb522f719-ac45-46a7-af43-2b87ee80cbf9/dqc_reference/reference_markers.hmm GCF_023074835.1_ASM2307483v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:06:10,679] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:06:10,680] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg613e98a3-924e-4535-aa28-7a5959e08317/GCF_023074835.1_ASM2307483v1_genomic.fna.gz]
[2024-01-25 19:06:10,719] [INFO] Query marker FASTA was written to GCF_023074835.1_ASM2307483v1_genomic.fna/markers.fasta
[2024-01-25 19:06:10,719] [INFO] Task started: Blastn
[2024-01-25 19:06:10,719] [INFO] Running command: blastn -query GCF_023074835.1_ASM2307483v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb522f719-ac45-46a7-af43-2b87ee80cbf9/dqc_reference/reference_markers.fasta -out GCF_023074835.1_ASM2307483v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:06:11,213] [INFO] Task succeeded: Blastn
[2024-01-25 19:06:11,215] [INFO] Selected 9 target genomes.
[2024-01-25 19:06:11,216] [INFO] Target genome list was writen to GCF_023074835.1_ASM2307483v1_genomic.fna/target_genomes.txt
[2024-01-25 19:06:11,220] [INFO] Task started: fastANI
[2024-01-25 19:06:11,220] [INFO] Running command: fastANI --query /var/lib/cwl/stg613e98a3-924e-4535-aa28-7a5959e08317/GCF_023074835.1_ASM2307483v1_genomic.fna.gz --refList GCF_023074835.1_ASM2307483v1_genomic.fna/target_genomes.txt --output GCF_023074835.1_ASM2307483v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:06:20,342] [INFO] Task succeeded: fastANI
[2024-01-25 19:06:20,343] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb522f719-ac45-46a7-af43-2b87ee80cbf9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:06:20,344] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb522f719-ac45-46a7-af43-2b87ee80cbf9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:06:20,360] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:06:20,360] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:06:20,360] [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
Halomarina salina	strain=ZS-57-S	GCA_023074835.1	1872699	1872699	type	True	100.0	1469	1483	95	conclusive
Halomarina rubra	strain=ZS-47-S	GCA_023699475.1	2071873	2071873	type	True	85.1497	934	1483	95	below_threshold
Halomarina oriensis	strain=JCM 16495	GCA_009791395.1	671145	671145	type	True	84.9224	891	1483	95	below_threshold
Haloprofundus halophilus	strain=NK23	GCA_003439925.1	2283527	2283527	type	True	78.5605	503	1483	95	below_threshold
Halostella litorea	strain=DLLS-108	GCA_004785955.1	2528831	2528831	type	True	78.3346	495	1483	95	below_threshold
Halomicroarcula nitratireducens	strain=F27	GCA_019599505.1	2487749	2487749	type	True	78.2819	488	1483	95	below_threshold
Halostella salina	strain=CBA1114	GCA_003675855.1	1547897	1547897	type	True	78.2395	490	1483	95	below_threshold
Halostella limicola	strain=LT12	GCA_003675875.1	2448456	2448456	type	True	78.1266	523	1483	95	below_threshold
Halosimplex halophilum	strain=TH32	GCA_004698125.1	2559572	2559572	type	True	77.8351	485	1483	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:06:20,362] [INFO] DFAST Taxonomy check result was written to GCF_023074835.1_ASM2307483v1_genomic.fna/tc_result.tsv
[2024-01-25 19:06:20,364] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:06:20,364] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:06:20,364] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb522f719-ac45-46a7-af43-2b87ee80cbf9/dqc_reference/checkm_data
[2024-01-25 19:06:20,365] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:06:20,411] [INFO] Task started: CheckM
[2024-01-25 19:06:20,411] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023074835.1_ASM2307483v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023074835.1_ASM2307483v1_genomic.fna/checkm_input GCF_023074835.1_ASM2307483v1_genomic.fna/checkm_result
[2024-01-25 19:07:10,183] [INFO] Task succeeded: CheckM
[2024-01-25 19:07:10,184] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:07:10,254] [INFO] ===== Completeness check finished =====
[2024-01-25 19:07:10,254] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:07:10,255] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023074835.1_ASM2307483v1_genomic.fna/markers.fasta)
[2024-01-25 19:07:10,255] [INFO] Task started: Blastn
[2024-01-25 19:07:10,255] [INFO] Running command: blastn -query GCF_023074835.1_ASM2307483v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb522f719-ac45-46a7-af43-2b87ee80cbf9/dqc_reference/reference_markers_gtdb.fasta -out GCF_023074835.1_ASM2307483v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:07:10,803] [INFO] Task succeeded: Blastn
[2024-01-25 19:07:10,807] [INFO] Selected 13 target genomes.
[2024-01-25 19:07:10,807] [INFO] Target genome list was writen to GCF_023074835.1_ASM2307483v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:07:10,830] [INFO] Task started: fastANI
[2024-01-25 19:07:10,831] [INFO] Running command: fastANI --query /var/lib/cwl/stg613e98a3-924e-4535-aa28-7a5959e08317/GCF_023074835.1_ASM2307483v1_genomic.fna.gz --refList GCF_023074835.1_ASM2307483v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023074835.1_ASM2307483v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:07:21,837] [INFO] Task succeeded: fastANI
[2024-01-25 19:07:21,849] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:07:21,850] [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_009791395.1	s__Halomarina oriensis	84.8984	893	1483	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003021975.1	s__Halomarina sp003021975	79.5168	506	1483	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004785955.1	s__Halostella litorea	78.2867	502	1483	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_003675855.1	s__Halostella salina	78.2512	488	1483	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_003675875.1	s__Halostella sp003675875	78.1513	519	1483	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_003298465.1	s__Haladaptatus sp003298465	78.13	521	1483	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Haladaptatus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010119195.1	s__Haloarcula salina	78.085	464	1483	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900114435.1	s__Halomicrobium zhouii	77.9555	463	1483	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004698125.1	s__Halosimplex halophilum	77.842	484	1483	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halosimplex	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102375.1	s__Halorubrum xinjiangense	77.5055	408	1483	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003021755.1	s__Halomicroarcula sp003021755	77.4723	248	1483	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halomicroarcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016065055.1	s__Halosimplex litoreum	77.4337	467	1483	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halosimplex	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000455345.1	s__Halopiger_A goleimassiliensis	77.1709	382	1483	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halopiger_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:07:21,853] [INFO] GTDB search result was written to GCF_023074835.1_ASM2307483v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:07:21,853] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:07:21,859] [INFO] DFAST_QC result json was written to GCF_023074835.1_ASM2307483v1_genomic.fna/dqc_result.json
[2024-01-25 19:07:21,859] [INFO] DFAST_QC completed!
[2024-01-25 19:07:21,859] [INFO] Total running time: 0h1m31s