[2024-01-24 10:57:50,257] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:50,260] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:50,260] [INFO] DQC Reference Directory: /var/lib/cwl/stg1fc78d38-d138-4716-8cdb-71ae971a49cd/dqc_reference
[2024-01-24 10:57:52,647] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:52,648] [INFO] Task started: Prodigal
[2024-01-24 10:57:52,649] [INFO] Running command: gunzip -c /var/lib/cwl/stg97d36b17-ff5a-420c-a2ce-d7de57b47969/GCF_016908315.1_ASM1690831v1_genomic.fna.gz | prodigal -d GCF_016908315.1_ASM1690831v1_genomic.fna/cds.fna -a GCF_016908315.1_ASM1690831v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:57,517] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:57,518] [INFO] Task started: HMMsearch
[2024-01-24 10:57:57,518] [INFO] Running command: hmmsearch --tblout GCF_016908315.1_ASM1690831v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1fc78d38-d138-4716-8cdb-71ae971a49cd/dqc_reference/reference_markers.hmm GCF_016908315.1_ASM1690831v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:57,792] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:57,793] [INFO] Found 6/6 markers.
[2024-01-24 10:57:57,826] [INFO] Query marker FASTA was written to GCF_016908315.1_ASM1690831v1_genomic.fna/markers.fasta
[2024-01-24 10:57:57,827] [INFO] Task started: Blastn
[2024-01-24 10:57:57,827] [INFO] Running command: blastn -query GCF_016908315.1_ASM1690831v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1fc78d38-d138-4716-8cdb-71ae971a49cd/dqc_reference/reference_markers.fasta -out GCF_016908315.1_ASM1690831v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:59,752] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:59,758] [INFO] Selected 22 target genomes.
[2024-01-24 10:57:59,758] [INFO] Target genome list was writen to GCF_016908315.1_ASM1690831v1_genomic.fna/target_genomes.txt
[2024-01-24 10:58:00,323] [INFO] Task started: fastANI
[2024-01-24 10:58:00,324] [INFO] Running command: fastANI --query /var/lib/cwl/stg97d36b17-ff5a-420c-a2ce-d7de57b47969/GCF_016908315.1_ASM1690831v1_genomic.fna.gz --refList GCF_016908315.1_ASM1690831v1_genomic.fna/target_genomes.txt --output GCF_016908315.1_ASM1690831v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:11,640] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:11,640] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1fc78d38-d138-4716-8cdb-71ae971a49cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:11,641] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1fc78d38-d138-4716-8cdb-71ae971a49cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:11,653] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:58:11,653] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:11,654] [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
Halanaerobacter jeridensis	strain=DSM 23230	GCA_016908315.1	706427	706427	type	True	100.0	1082	1082	95	conclusive
Halobacteroides halobius	strain=DSM 5150	GCA_000328625.1	42422	42422	type	True	76.7071	186	1082	95	below_threshold
Orenia marismortui	strain=DSM 5156	GCA_000379025.1	46469	46469	type	True	76.1835	145	1082	95	below_threshold
Natroniella acetigena	strain=Z-7937	GCA_023227745.1	52004	52004	type	True	76.1232	92	1082	95	below_threshold
Halonatronum saccharophilum	strain=DSM 13868	GCA_000517025.1	150060	150060	type	True	75.9957	83	1082	95	below_threshold
Orenia metallireducens	strain=Z6	GCA_001693735.1	1413210	1413210	type	True	75.8223	102	1082	95	below_threshold
Selenihalanaerobacter shriftii	strain=ATCC BAA-73	GCA_900167185.1	142842	142842	type	True	75.5503	105	1082	95	below_threshold
Halanaerobium praevalens	strain=DSM 2228	GCA_000165465.1	2331	2331	type	True	75.1369	75	1082	95	below_threshold
Halanaerobium salsuginis	strain=ATCC 51327	GCA_900114545.1	29563	29563	type	True	74.9915	51	1082	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:11,656] [INFO] DFAST Taxonomy check result was written to GCF_016908315.1_ASM1690831v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:11,657] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:11,657] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:11,657] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1fc78d38-d138-4716-8cdb-71ae971a49cd/dqc_reference/checkm_data
[2024-01-24 10:58:11,658] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:11,694] [INFO] Task started: CheckM
[2024-01-24 10:58:11,694] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016908315.1_ASM1690831v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016908315.1_ASM1690831v1_genomic.fna/checkm_input GCF_016908315.1_ASM1690831v1_genomic.fna/checkm_result
[2024-01-24 10:58:33,752] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:33,753] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:33,779] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:33,780] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:33,780] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016908315.1_ASM1690831v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:33,781] [INFO] Task started: Blastn
[2024-01-24 10:58:33,781] [INFO] Running command: blastn -query GCF_016908315.1_ASM1690831v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1fc78d38-d138-4716-8cdb-71ae971a49cd/dqc_reference/reference_markers_gtdb.fasta -out GCF_016908315.1_ASM1690831v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:34,886] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:34,894] [INFO] Selected 27 target genomes.
[2024-01-24 10:58:34,895] [INFO] Target genome list was writen to GCF_016908315.1_ASM1690831v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:34,933] [INFO] Task started: fastANI
[2024-01-24 10:58:34,933] [INFO] Running command: fastANI --query /var/lib/cwl/stg97d36b17-ff5a-420c-a2ce-d7de57b47969/GCF_016908315.1_ASM1690831v1_genomic.fna.gz --refList GCF_016908315.1_ASM1690831v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016908315.1_ASM1690831v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:47,313] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:47,325] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:47,325] [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_016908315.1	s__Halanaerobacter jeridensis	100.0	1082	1082	d__Bacteria;p__Firmicutes_F;c__Halanaerobiia;o__Halobacteroidales;f__Halobacteroidaceae;g__Halanaerobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000328625.1	s__Halobacteroides halobius	76.7197	185	1082	d__Bacteria;p__Firmicutes_F;c__Halanaerobiia;o__Halobacteroidales;f__Halobacteroidaceae;g__Halobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379025.1	s__Orenia marismortui	76.2016	142	1082	d__Bacteria;p__Firmicutes_F;c__Halanaerobiia;o__Halobacteroidales;f__Halobacteroidaceae;g__Orenia	95.0	96.95	96.95	0.88	0.88	2	-
GCF_016908635.1	s__Sporohalobacter salinus	76.0115	100	1082	d__Bacteria;p__Firmicutes_F;c__Halanaerobiia;o__Halobacteroidales;f__Acetohalobiaceae;g__Sporohalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000517025.1	s__Halonatronum saccharophilum	75.9957	83	1082	d__Bacteria;p__Firmicutes_F;c__Halanaerobiia;o__Halobacteroidales;f__Halobacteroidaceae;g__Halonatronum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167185.1	s__Selenihalanaerobacter shriftii	75.5503	105	1082	d__Bacteria;p__Firmicutes_F;c__Halanaerobiia;o__Halobacteroidales;f__Acetohalobiaceae;g__Selenihalanaerobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000165465.1	s__Halanaerobium praevalens	75.1305	76	1082	d__Bacteria;p__Firmicutes_F;c__Halanaerobiia;o__Halanaerobiales;f__Halanaerobiaceae;g__Halanaerobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114545.1	s__Halanaerobium salsuginis	74.9915	51	1082	d__Bacteria;p__Firmicutes_F;c__Halanaerobiia;o__Halanaerobiales;f__Halanaerobiaceae;g__Halanaerobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:47,327] [INFO] GTDB search result was written to GCF_016908315.1_ASM1690831v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:47,328] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:47,332] [INFO] DFAST_QC result json was written to GCF_016908315.1_ASM1690831v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:47,333] [INFO] DFAST_QC completed!
[2024-01-24 10:58:47,333] [INFO] Total running time: 0h0m57s