[2024-01-25 19:03:20,861] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:03:20,865] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:03:20,865] [INFO] DQC Reference Directory: /var/lib/cwl/stg66db2a16-755d-4b99-be73-f8309e0adcc0/dqc_reference
[2024-01-25 19:03:22,010] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:03:22,010] [INFO] Task started: Prodigal
[2024-01-25 19:03:22,010] [INFO] Running command: gunzip -c /var/lib/cwl/stg90174717-ce33-4d75-aa99-f44b6fd6ad8d/GCF_000336775.1_ASM33677v1_genomic.fna.gz | prodigal -d GCF_000336775.1_ASM33677v1_genomic.fna/cds.fna -a GCF_000336775.1_ASM33677v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:03:38,057] [INFO] Task succeeded: Prodigal
[2024-01-25 19:03:38,057] [INFO] Task started: HMMsearch
[2024-01-25 19:03:38,058] [INFO] Running command: hmmsearch --tblout GCF_000336775.1_ASM33677v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg66db2a16-755d-4b99-be73-f8309e0adcc0/dqc_reference/reference_markers.hmm GCF_000336775.1_ASM33677v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:03:38,335] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:03:38,336] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg90174717-ce33-4d75-aa99-f44b6fd6ad8d/GCF_000336775.1_ASM33677v1_genomic.fna.gz]
[2024-01-25 19:03:38,373] [INFO] Query marker FASTA was written to GCF_000336775.1_ASM33677v1_genomic.fna/markers.fasta
[2024-01-25 19:03:38,374] [INFO] Task started: Blastn
[2024-01-25 19:03:38,374] [INFO] Running command: blastn -query GCF_000336775.1_ASM33677v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg66db2a16-755d-4b99-be73-f8309e0adcc0/dqc_reference/reference_markers.fasta -out GCF_000336775.1_ASM33677v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:03:38,886] [INFO] Task succeeded: Blastn
[2024-01-25 19:03:38,889] [INFO] Selected 8 target genomes.
[2024-01-25 19:03:38,889] [INFO] Target genome list was writen to GCF_000336775.1_ASM33677v1_genomic.fna/target_genomes.txt
[2024-01-25 19:03:38,899] [INFO] Task started: fastANI
[2024-01-25 19:03:38,899] [INFO] Running command: fastANI --query /var/lib/cwl/stg90174717-ce33-4d75-aa99-f44b6fd6ad8d/GCF_000336775.1_ASM33677v1_genomic.fna.gz --refList GCF_000336775.1_ASM33677v1_genomic.fna/target_genomes.txt --output GCF_000336775.1_ASM33677v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:03:48,705] [INFO] Task succeeded: fastANI
[2024-01-25 19:03:48,705] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg66db2a16-755d-4b99-be73-f8309e0adcc0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:03:48,705] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg66db2a16-755d-4b99-be73-f8309e0adcc0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:03:48,711] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:03:48,712] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 19:03:48,712] [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
Haloferax gibbonsii	strain=ATCC 33959	GCA_000336775.1	35746	35746	type	True	100.0	1337	1338	95	inconclusive
Haloferax prahovense	strain=DSM 18310	GCA_000336815.1	381852	381852	type	True	96.8304	1159	1338	95	inconclusive
Haloferax marisrubri	strain=SB3	GCA_001469875.2	1544719	1544719	type	True	94.3534	1100	1338	95	below_threshold
Haloferax sulfurifontis	strain=ATCC BAA-897	GCA_000337835.1	255616	255616	type	True	93.6748	1005	1338	95	below_threshold
Haloferax sulfurifontis	strain=CCM 7217	GCA_014635105.1	255616	255616	type	True	93.651	1041	1338	95	below_threshold
Haloferax massiliensis	strain=Arc-Hr	GCA_001368915.1	1476858	1476858	type	True	93.5178	1092	1338	95	below_threshold
Haloferax volcanii	strain=DS2	GCA_000337315.1	2246	2246	type	True	93.3208	1022	1338	95	below_threshold
Haloferax volcanii	strain=DS2	GCA_000025685.1	2246	2246	type	True	93.2931	1059	1338	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:03:48,713] [INFO] DFAST Taxonomy check result was written to GCF_000336775.1_ASM33677v1_genomic.fna/tc_result.tsv
[2024-01-25 19:03:48,713] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:03:48,713] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:03:48,714] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg66db2a16-755d-4b99-be73-f8309e0adcc0/dqc_reference/checkm_data
[2024-01-25 19:03:48,714] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:03:48,756] [INFO] Task started: CheckM
[2024-01-25 19:03:48,756] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000336775.1_ASM33677v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000336775.1_ASM33677v1_genomic.fna/checkm_input GCF_000336775.1_ASM33677v1_genomic.fna/checkm_result
[2024-01-25 19:04:32,447] [INFO] Task succeeded: CheckM
[2024-01-25 19:04:32,448] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:04:32,466] [INFO] ===== Completeness check finished =====
[2024-01-25 19:04:32,466] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:04:32,467] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000336775.1_ASM33677v1_genomic.fna/markers.fasta)
[2024-01-25 19:04:32,467] [INFO] Task started: Blastn
[2024-01-25 19:04:32,467] [INFO] Running command: blastn -query GCF_000336775.1_ASM33677v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg66db2a16-755d-4b99-be73-f8309e0adcc0/dqc_reference/reference_markers_gtdb.fasta -out GCF_000336775.1_ASM33677v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:04:33,005] [INFO] Task succeeded: Blastn
[2024-01-25 19:04:33,008] [INFO] Selected 7 target genomes.
[2024-01-25 19:04:33,008] [INFO] Target genome list was writen to GCF_000336775.1_ASM33677v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:04:33,010] [INFO] Task started: fastANI
[2024-01-25 19:04:33,010] [INFO] Running command: fastANI --query /var/lib/cwl/stg90174717-ce33-4d75-aa99-f44b6fd6ad8d/GCF_000336775.1_ASM33677v1_genomic.fna.gz --refList GCF_000336775.1_ASM33677v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000336775.1_ASM33677v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:04:41,436] [INFO] Task succeeded: fastANI
[2024-01-25 19:04:41,441] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:04:41,441] [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_000336775.1	s__Haloferax gibbonsii	100.0	1337	1338	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	96.8304	98.89	98.78	0.89	0.88	5	conclusive
GCF_000336815.1	s__Haloferax prahovense	96.8304	1159	1338	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	96.8304	99.29	99.22	0.91	0.91	5	conclusive
GCF_001482285.1	s__Haloferax sp001482285	94.7641	1106	1338	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001469875.2	s__Haloferax marisrubri	94.3392	1101	1338	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	95.0	95.85	95.85	0.83	0.83	2	-
GCF_000337835.1	s__Haloferax sulfurifontis	93.6562	1006	1338	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	96.9285	99.04	99.04	0.92	0.92	2	-
GCF_001368915.1	s__Haloferax massiliensis	93.5163	1093	1338	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	95.2845	98.47	96.94	0.94	0.88	3	-
GCF_000025685.1	s__Haloferax volcanii	93.3053	1058	1338	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	95.0	98.27	96.62	0.93	0.89	21	-
--------------------------------------------------------------------------------
[2024-01-25 19:04:41,443] [INFO] GTDB search result was written to GCF_000336775.1_ASM33677v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:04:41,443] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:04:41,445] [INFO] DFAST_QC result json was written to GCF_000336775.1_ASM33677v1_genomic.fna/dqc_result.json
[2024-01-25 19:04:41,445] [INFO] DFAST_QC completed!
[2024-01-25 19:04:41,445] [INFO] Total running time: 0h1m21s