[2024-01-25 18:03:35,628] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:03:35,630] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:03:35,631] [INFO] DQC Reference Directory: /var/lib/cwl/stg40328a7d-b518-4023-bb17-cbfd82b7bd5a/dqc_reference
[2024-01-25 18:03:36,763] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:03:36,763] [INFO] Task started: Prodigal
[2024-01-25 18:03:36,764] [INFO] Running command: gunzip -c /var/lib/cwl/stg8175f0e5-c2ac-4658-803f-9e9857a59835/GCF_002201795.1_ASM220179v1_genomic.fna.gz | prodigal -d GCF_002201795.1_ASM220179v1_genomic.fna/cds.fna -a GCF_002201795.1_ASM220179v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:03:54,861] [INFO] Task succeeded: Prodigal
[2024-01-25 18:03:54,861] [INFO] Task started: HMMsearch
[2024-01-25 18:03:54,861] [INFO] Running command: hmmsearch --tblout GCF_002201795.1_ASM220179v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg40328a7d-b518-4023-bb17-cbfd82b7bd5a/dqc_reference/reference_markers.hmm GCF_002201795.1_ASM220179v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:03:55,133] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:03:55,134] [INFO] Found 6/6 markers.
[2024-01-25 18:03:55,174] [INFO] Query marker FASTA was written to GCF_002201795.1_ASM220179v1_genomic.fna/markers.fasta
[2024-01-25 18:03:55,174] [INFO] Task started: Blastn
[2024-01-25 18:03:55,174] [INFO] Running command: blastn -query GCF_002201795.1_ASM220179v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg40328a7d-b518-4023-bb17-cbfd82b7bd5a/dqc_reference/reference_markers.fasta -out GCF_002201795.1_ASM220179v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:03:55,723] [INFO] Task succeeded: Blastn
[2024-01-25 18:03:55,726] [INFO] Selected 18 target genomes.
[2024-01-25 18:03:55,726] [INFO] Target genome list was writen to GCF_002201795.1_ASM220179v1_genomic.fna/target_genomes.txt
[2024-01-25 18:03:55,737] [INFO] Task started: fastANI
[2024-01-25 18:03:55,737] [INFO] Running command: fastANI --query /var/lib/cwl/stg8175f0e5-c2ac-4658-803f-9e9857a59835/GCF_002201795.1_ASM220179v1_genomic.fna.gz --refList GCF_002201795.1_ASM220179v1_genomic.fna/target_genomes.txt --output GCF_002201795.1_ASM220179v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:04:10,755] [INFO] Task succeeded: fastANI
[2024-01-25 18:04:10,755] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg40328a7d-b518-4023-bb17-cbfd82b7bd5a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:04:10,756] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg40328a7d-b518-4023-bb17-cbfd82b7bd5a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:04:10,762] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:04:10,762] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:04:10,762] [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
Alkalitalea saponilacus	strain=SC/BZ-SP2	GCA_002201795.1	889453	889453	type	True	100.0	1589	1591	95	conclusive
Alkalitalea saponilacus	strain=DSM 24412	GCA_900168165.1	889453	889453	type	True	99.9414	1471	1591	95	conclusive
Alkaliflexus imshenetskii	strain=Z-7010	GCA_000517065.1	286730	286730	type	True	77.7254	161	1591	95	below_threshold
Geofilum rhodophaeum	strain=HF401	GCA_002210225.1	1965019	1965019	type	True	77.613	103	1591	95	below_threshold
Geofilum rubicundum	strain=JCM 15548	GCA_000974365.1	472113	472113	type	True	76.9822	144	1591	95	below_threshold
Marinilabilia rubra	strain=WTE16	GCA_003121985.1	2162893	2162893	type	True	76.3901	76	1591	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:04:10,763] [INFO] DFAST Taxonomy check result was written to GCF_002201795.1_ASM220179v1_genomic.fna/tc_result.tsv
[2024-01-25 18:04:10,764] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:04:10,764] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:04:10,764] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg40328a7d-b518-4023-bb17-cbfd82b7bd5a/dqc_reference/checkm_data
[2024-01-25 18:04:10,765] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:04:10,810] [INFO] Task started: CheckM
[2024-01-25 18:04:10,810] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002201795.1_ASM220179v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002201795.1_ASM220179v1_genomic.fna/checkm_input GCF_002201795.1_ASM220179v1_genomic.fna/checkm_result
[2024-01-25 18:05:04,039] [INFO] Task succeeded: CheckM
[2024-01-25 18:05:04,040] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:05:04,064] [INFO] ===== Completeness check finished =====
[2024-01-25 18:05:04,065] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:05:04,065] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002201795.1_ASM220179v1_genomic.fna/markers.fasta)
[2024-01-25 18:05:04,065] [INFO] Task started: Blastn
[2024-01-25 18:05:04,065] [INFO] Running command: blastn -query GCF_002201795.1_ASM220179v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg40328a7d-b518-4023-bb17-cbfd82b7bd5a/dqc_reference/reference_markers_gtdb.fasta -out GCF_002201795.1_ASM220179v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:05:04,848] [INFO] Task succeeded: Blastn
[2024-01-25 18:05:04,851] [INFO] Selected 21 target genomes.
[2024-01-25 18:05:04,852] [INFO] Target genome list was writen to GCF_002201795.1_ASM220179v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:05:04,864] [INFO] Task started: fastANI
[2024-01-25 18:05:04,865] [INFO] Running command: fastANI --query /var/lib/cwl/stg8175f0e5-c2ac-4658-803f-9e9857a59835/GCF_002201795.1_ASM220179v1_genomic.fna.gz --refList GCF_002201795.1_ASM220179v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002201795.1_ASM220179v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:05:20,254] [INFO] Task succeeded: fastANI
[2024-01-25 18:05:20,262] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:05:20,262] [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_002201795.1	s__Natronoflexus saponilacus	100.0	1591	1591	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Natronoflexus	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_004345615.1	s__Natronoflexus pectinivorans	89.8433	1250	1591	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Natronoflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000517065.1	s__Alkaliflexus imshenetskii	77.7698	161	1591	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Alkaliflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002210225.1	s__Geofilum rhodophaeum	77.6577	103	1591	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Geofilum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000974365.1	s__Geofilum rubicundum	76.9658	145	1591	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Geofilum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002412555.1	s__Geofilum sp002412555	76.6119	122	1591	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Geofilum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:05:20,264] [INFO] GTDB search result was written to GCF_002201795.1_ASM220179v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:05:20,265] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:05:20,275] [INFO] DFAST_QC result json was written to GCF_002201795.1_ASM220179v1_genomic.fna/dqc_result.json
[2024-01-25 18:05:20,276] [INFO] DFAST_QC completed!
[2024-01-25 18:05:20,276] [INFO] Total running time: 0h1m45s