[2024-01-25 18:13:05,961] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:13:05,971] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:13:05,971] [INFO] DQC Reference Directory: /var/lib/cwl/stgc32dac3d-3a62-4dbb-b7e9-d260f79de01c/dqc_reference
[2024-01-25 18:13:07,154] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:13:07,154] [INFO] Task started: Prodigal
[2024-01-25 18:13:07,155] [INFO] Running command: gunzip -c /var/lib/cwl/stgca74e89e-0b7f-435e-a4a6-080c94206864/GCF_026586625.1_ASM2658662v1_genomic.fna.gz | prodigal -d GCF_026586625.1_ASM2658662v1_genomic.fna/cds.fna -a GCF_026586625.1_ASM2658662v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:13:24,967] [INFO] Task succeeded: Prodigal
[2024-01-25 18:13:24,967] [INFO] Task started: HMMsearch
[2024-01-25 18:13:24,968] [INFO] Running command: hmmsearch --tblout GCF_026586625.1_ASM2658662v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc32dac3d-3a62-4dbb-b7e9-d260f79de01c/dqc_reference/reference_markers.hmm GCF_026586625.1_ASM2658662v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:13:25,254] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:13:25,255] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgca74e89e-0b7f-435e-a4a6-080c94206864/GCF_026586625.1_ASM2658662v1_genomic.fna.gz]
[2024-01-25 18:13:25,293] [INFO] Query marker FASTA was written to GCF_026586625.1_ASM2658662v1_genomic.fna/markers.fasta
[2024-01-25 18:13:25,293] [INFO] Task started: Blastn
[2024-01-25 18:13:25,293] [INFO] Running command: blastn -query GCF_026586625.1_ASM2658662v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc32dac3d-3a62-4dbb-b7e9-d260f79de01c/dqc_reference/reference_markers.fasta -out GCF_026586625.1_ASM2658662v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:13:25,809] [INFO] Task succeeded: Blastn
[2024-01-25 18:13:25,812] [INFO] Selected 14 target genomes.
[2024-01-25 18:13:25,812] [INFO] Target genome list was writen to GCF_026586625.1_ASM2658662v1_genomic.fna/target_genomes.txt
[2024-01-25 18:13:25,845] [INFO] Task started: fastANI
[2024-01-25 18:13:25,845] [INFO] Running command: fastANI --query /var/lib/cwl/stgca74e89e-0b7f-435e-a4a6-080c94206864/GCF_026586625.1_ASM2658662v1_genomic.fna.gz --refList GCF_026586625.1_ASM2658662v1_genomic.fna/target_genomes.txt --output GCF_026586625.1_ASM2658662v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:13:39,939] [INFO] Task succeeded: fastANI
[2024-01-25 18:13:39,939] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc32dac3d-3a62-4dbb-b7e9-d260f79de01c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:13:39,940] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc32dac3d-3a62-4dbb-b7e9-d260f79de01c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:13:39,951] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:13:39,951] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:13:39,951] [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
Halogranum amylolyticum	strain=CGMCC 1.10121	GCA_900110465.1	660520	660520	type	True	79.78	670	1480	95	below_threshold
Haloprofundus halophilus	strain=NK23	GCA_003439925.1	2283527	2283527	type	True	79.7048	605	1480	95	below_threshold
Halegenticoccus soli	strain=SYSU A9-0	GCA_002844195.1	1985678	1985678	type	True	79.353	663	1480	95	below_threshold
Halogranum rubrum	strain=CGMCC 1.7738	GCA_900114455.1	553466	553466	type	True	79.1095	651	1480	95	below_threshold
Halogranum salarium	strain=B-1	GCA_000283335.1	693851	693851	type	True	79.0356	651	1480	95	below_threshold
Halegenticoccus tardaugens	strain=SYSU A00711	GCA_004116405.1	2071624	2071624	type	True	79.0317	626	1480	95	below_threshold
Haloprofundus marisrubri	strain=SB9	GCA_001469955.1	1514971	1514971	type	True	78.8935	569	1480	95	below_threshold
Halobellus limi	strain=CGMCC 1.10331	GCA_900108165.1	699433	699433	type	True	78.3551	511	1480	95	below_threshold
Halobellus limi	strain=CGMCC 1.10331	GCA_004799685.1	699433	699433	type	True	78.3528	503	1480	95	below_threshold
Salinigranum salinum	strain=YJ-50-S2	GCA_009176545.1	1364937	1364937	type	True	78.2624	585	1480	95	below_threshold
Halobellus litoreus	strain=GX31	GCA_024464595.1	755310	755310	type	True	78.2587	467	1480	95	below_threshold
Halorubrum lipolyticum	strain=DSM 21995	GCA_000337375.1	368624	368624	type	True	78.0239	476	1480	95	below_threshold
Natronomonas salina	strain=YPL13	GCA_013391105.1	1710540	1710540	type	True	78.0183	461	1480	95	below_threshold
Halorubrum persicum	strain=C49	GCA_002727125.1	1383844	1383844	type	True	77.9919	453	1480	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:13:39,955] [INFO] DFAST Taxonomy check result was written to GCF_026586625.1_ASM2658662v1_genomic.fna/tc_result.tsv
[2024-01-25 18:13:39,955] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:13:39,956] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:13:39,956] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc32dac3d-3a62-4dbb-b7e9-d260f79de01c/dqc_reference/checkm_data
[2024-01-25 18:13:39,957] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:13:40,002] [INFO] Task started: CheckM
[2024-01-25 18:13:40,002] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026586625.1_ASM2658662v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026586625.1_ASM2658662v1_genomic.fna/checkm_input GCF_026586625.1_ASM2658662v1_genomic.fna/checkm_result
[2024-01-25 18:14:27,523] [INFO] Task succeeded: CheckM
[2024-01-25 18:14:27,524] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:14:27,557] [INFO] ===== Completeness check finished =====
[2024-01-25 18:14:27,557] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:14:27,558] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026586625.1_ASM2658662v1_genomic.fna/markers.fasta)
[2024-01-25 18:14:27,559] [INFO] Task started: Blastn
[2024-01-25 18:14:27,559] [INFO] Running command: blastn -query GCF_026586625.1_ASM2658662v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc32dac3d-3a62-4dbb-b7e9-d260f79de01c/dqc_reference/reference_markers_gtdb.fasta -out GCF_026586625.1_ASM2658662v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:14:28,132] [INFO] Task succeeded: Blastn
[2024-01-25 18:14:28,137] [INFO] Selected 14 target genomes.
[2024-01-25 18:14:28,137] [INFO] Target genome list was writen to GCF_026586625.1_ASM2658662v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:14:28,148] [INFO] Task started: fastANI
[2024-01-25 18:14:28,148] [INFO] Running command: fastANI --query /var/lib/cwl/stgca74e89e-0b7f-435e-a4a6-080c94206864/GCF_026586625.1_ASM2658662v1_genomic.fna.gz --refList GCF_026586625.1_ASM2658662v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026586625.1_ASM2658662v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:14:41,331] [INFO] Task succeeded: fastANI
[2024-01-25 18:14:41,340] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:14:41,340] [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_900110465.1	s__Halogranum amylolyticum	79.7323	675	1480	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halogranum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003439925.1	s__Haloprofundus halophilus	79.6799	608	1480	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloprofundus	95.0	98.76	98.76	0.93	0.93	2	-
GCF_002844195.1	s__Halegenticoccus soli	79.3169	669	1480	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halegenticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114455.1	s__Halogranum rubrum	79.1349	646	1480	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halogranum	95.0	97.00	97.00	0.87	0.87	2	-
GCA_004116405.1	s__Halegenticoccus sp004116405	79.0196	626	1480	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halegenticoccus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001469955.1	s__Haloprofundus marisrubri	78.8749	572	1480	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloprofundus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112175.1	s__Halogeometricum rufum	78.8357	648	1480	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halogeometricum	95.0	98.26	98.26	0.87	0.87	2	-
GCF_002906575.1	s__Salinigranum rubrum	78.7719	626	1480	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Salinigranum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013401515.1	s__Halobaculum sp013401515	78.6231	582	1480	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004799685.1	s__Halobellus limi	78.3801	499	1480	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halobellus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_009176545.1	s__Salinigranum salinum	78.2364	588	1480	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Salinigranum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013391105.1	s__Natronomonas salina	78.0412	458	1480	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002727125.1	s__Halorubrum persicum	78.0	454	1480	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000337375.1	s__Halorubrum lipolyticum	77.9824	483	1480	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:14:41,342] [INFO] GTDB search result was written to GCF_026586625.1_ASM2658662v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:14:41,342] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:14:41,346] [INFO] DFAST_QC result json was written to GCF_026586625.1_ASM2658662v1_genomic.fna/dqc_result.json
[2024-01-25 18:14:41,346] [INFO] DFAST_QC completed!
[2024-01-25 18:14:41,346] [INFO] Total running time: 0h1m35s