[2024-01-25 19:35:05,757] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:35:05,759] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:35:05,759] [INFO] DQC Reference Directory: /var/lib/cwl/stg79b19d42-6a84-4444-a6ba-c2c08ab14331/dqc_reference
[2024-01-25 19:35:06,899] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:35:06,899] [INFO] Task started: Prodigal
[2024-01-25 19:35:06,899] [INFO] Running command: gunzip -c /var/lib/cwl/stg6f8a088f-808d-4b66-8e84-920f6b55f11a/GCF_014075995.1_ASM1407599v1_genomic.fna.gz | prodigal -d GCF_014075995.1_ASM1407599v1_genomic.fna/cds.fna -a GCF_014075995.1_ASM1407599v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:35:27,008] [INFO] Task succeeded: Prodigal
[2024-01-25 19:35:27,009] [INFO] Task started: HMMsearch
[2024-01-25 19:35:27,009] [INFO] Running command: hmmsearch --tblout GCF_014075995.1_ASM1407599v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg79b19d42-6a84-4444-a6ba-c2c08ab14331/dqc_reference/reference_markers.hmm GCF_014075995.1_ASM1407599v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:35:27,294] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:35:27,295] [INFO] Found 6/6 markers.
[2024-01-25 19:35:27,348] [INFO] Query marker FASTA was written to GCF_014075995.1_ASM1407599v1_genomic.fna/markers.fasta
[2024-01-25 19:35:27,348] [INFO] Task started: Blastn
[2024-01-25 19:35:27,348] [INFO] Running command: blastn -query GCF_014075995.1_ASM1407599v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg79b19d42-6a84-4444-a6ba-c2c08ab14331/dqc_reference/reference_markers.fasta -out GCF_014075995.1_ASM1407599v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:35:27,899] [INFO] Task succeeded: Blastn
[2024-01-25 19:35:27,902] [INFO] Selected 15 target genomes.
[2024-01-25 19:35:27,902] [INFO] Target genome list was writen to GCF_014075995.1_ASM1407599v1_genomic.fna/target_genomes.txt
[2024-01-25 19:35:27,909] [INFO] Task started: fastANI
[2024-01-25 19:35:27,909] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f8a088f-808d-4b66-8e84-920f6b55f11a/GCF_014075995.1_ASM1407599v1_genomic.fna.gz --refList GCF_014075995.1_ASM1407599v1_genomic.fna/target_genomes.txt --output GCF_014075995.1_ASM1407599v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:35:46,856] [INFO] Task succeeded: fastANI
[2024-01-25 19:35:46,856] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg79b19d42-6a84-4444-a6ba-c2c08ab14331/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:35:46,857] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg79b19d42-6a84-4444-a6ba-c2c08ab14331/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:35:46,866] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:35:46,866] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:35:46,866] [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
Adhaeribacter radiodurans	strain=KUDC8001	GCA_014075995.1	2745197	2745197	type	True	100.0	2309	2311	95	conclusive
Adhaeribacter arboris	strain=HMF7605	GCA_003023845.1	2072846	2072846	type	True	81.7139	1498	2311	95	below_threshold
Adhaeribacter swui	strain=KCTC 52873	GCA_014217805.1	2086471	2086471	type	True	80.8286	1097	2311	95	below_threshold
Adhaeribacter pallidiroseus	strain=HMF7616	GCA_003340495.1	2072847	2072847	type	True	79.4826	965	2311	95	below_threshold
Adhaeribacter rhizoryzae	strain=DK36	GCA_008629685.1	2607907	2607907	type	True	77.1723	447	2311	95	below_threshold
Pontibacter arcticus	strain=2b14	GCA_003284895.1	2080288	2080288	type	True	76.5491	83	2311	95	below_threshold
Pontibacter mangrovi	strain=HB172049	GCA_006385705.1	2589816	2589816	type	True	76.1417	56	2311	95	below_threshold
Adhaeribacter soli	strain=MA2	GCA_008727925.1	2607655	2607655	type	True	76.0504	120	2311	95	below_threshold
Pontibacter silvestris	strain=XAAS-R86T	GCA_020907275.1	2305183	2305183	type	True	75.8852	65	2311	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:35:46,868] [INFO] DFAST Taxonomy check result was written to GCF_014075995.1_ASM1407599v1_genomic.fna/tc_result.tsv
[2024-01-25 19:35:46,868] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:35:46,868] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:35:46,868] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg79b19d42-6a84-4444-a6ba-c2c08ab14331/dqc_reference/checkm_data
[2024-01-25 19:35:46,869] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:35:46,933] [INFO] Task started: CheckM
[2024-01-25 19:35:46,933] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014075995.1_ASM1407599v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014075995.1_ASM1407599v1_genomic.fna/checkm_input GCF_014075995.1_ASM1407599v1_genomic.fna/checkm_result
[2024-01-25 19:36:41,829] [INFO] Task succeeded: CheckM
[2024-01-25 19:36:41,830] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:36:41,848] [INFO] ===== Completeness check finished =====
[2024-01-25 19:36:41,849] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:36:41,849] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014075995.1_ASM1407599v1_genomic.fna/markers.fasta)
[2024-01-25 19:36:41,850] [INFO] Task started: Blastn
[2024-01-25 19:36:41,850] [INFO] Running command: blastn -query GCF_014075995.1_ASM1407599v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg79b19d42-6a84-4444-a6ba-c2c08ab14331/dqc_reference/reference_markers_gtdb.fasta -out GCF_014075995.1_ASM1407599v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:36:42,587] [INFO] Task succeeded: Blastn
[2024-01-25 19:36:42,590] [INFO] Selected 11 target genomes.
[2024-01-25 19:36:42,590] [INFO] Target genome list was writen to GCF_014075995.1_ASM1407599v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:36:42,596] [INFO] Task started: fastANI
[2024-01-25 19:36:42,596] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f8a088f-808d-4b66-8e84-920f6b55f11a/GCF_014075995.1_ASM1407599v1_genomic.fna.gz --refList GCF_014075995.1_ASM1407599v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014075995.1_ASM1407599v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:36:56,694] [INFO] Task succeeded: fastANI
[2024-01-25 19:36:56,699] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:36:56,700] [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_014075995.1	s__Adhaeribacter radiodurans	100.0	2310	2311	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Adhaeribacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003023845.1	s__Adhaeribacter arboris	81.7204	1495	2311	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Adhaeribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014217805.1	s__Adhaeribacter swui	80.8187	1098	2311	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Adhaeribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003340495.1	s__Adhaeribacter pallidiroseus	79.4661	969	2311	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Adhaeribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008629685.1	s__Adhaeribacter rhizoryzae	77.1715	448	2311	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Adhaeribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473365.1	s__Adhaeribacter aquaticus	76.7239	230	2311	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Adhaeribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008727925.1	s__Adhaeribacter_A soli	76.0373	121	2311	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Adhaeribacter_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:36:56,701] [INFO] GTDB search result was written to GCF_014075995.1_ASM1407599v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:36:56,704] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:36:56,708] [INFO] DFAST_QC result json was written to GCF_014075995.1_ASM1407599v1_genomic.fna/dqc_result.json
[2024-01-25 19:36:56,708] [INFO] DFAST_QC completed!
[2024-01-25 19:36:56,708] [INFO] Total running time: 0h1m51s