[2024-01-24 11:58:57,341] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:58:57,343] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:58:57,344] [INFO] DQC Reference Directory: /var/lib/cwl/stg0b765ddf-35d1-4021-916e-fff16a215cdd/dqc_reference
[2024-01-24 11:58:58,603] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:58:58,604] [INFO] Task started: Prodigal
[2024-01-24 11:58:58,604] [INFO] Running command: gunzip -c /var/lib/cwl/stg977cfc17-82e6-4f00-a831-a170045d6f2e/GCF_007991635.1_ASM799163v1_genomic.fna.gz | prodigal -d GCF_007991635.1_ASM799163v1_genomic.fna/cds.fna -a GCF_007991635.1_ASM799163v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:23,865] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:23,866] [INFO] Task started: HMMsearch
[2024-01-24 11:59:23,866] [INFO] Running command: hmmsearch --tblout GCF_007991635.1_ASM799163v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0b765ddf-35d1-4021-916e-fff16a215cdd/dqc_reference/reference_markers.hmm GCF_007991635.1_ASM799163v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:24,238] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:24,239] [INFO] Found 6/6 markers.
[2024-01-24 11:59:24,308] [INFO] Query marker FASTA was written to GCF_007991635.1_ASM799163v1_genomic.fna/markers.fasta
[2024-01-24 11:59:24,309] [INFO] Task started: Blastn
[2024-01-24 11:59:24,309] [INFO] Running command: blastn -query GCF_007991635.1_ASM799163v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b765ddf-35d1-4021-916e-fff16a215cdd/dqc_reference/reference_markers.fasta -out GCF_007991635.1_ASM799163v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:24,965] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:24,968] [INFO] Selected 14 target genomes.
[2024-01-24 11:59:24,969] [INFO] Target genome list was writen to GCF_007991635.1_ASM799163v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:24,976] [INFO] Task started: fastANI
[2024-01-24 11:59:24,977] [INFO] Running command: fastANI --query /var/lib/cwl/stg977cfc17-82e6-4f00-a831-a170045d6f2e/GCF_007991635.1_ASM799163v1_genomic.fna.gz --refList GCF_007991635.1_ASM799163v1_genomic.fna/target_genomes.txt --output GCF_007991635.1_ASM799163v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:39,748] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:39,748] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0b765ddf-35d1-4021-916e-fff16a215cdd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:39,749] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0b765ddf-35d1-4021-916e-fff16a215cdd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:39,760] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:59:39,760] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:39,760] [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 aerolatus	strain=NBRC 106133	GCA_007991635.1	670289	670289	type	True	100.0	2174	2179	95	conclusive
Adhaeribacter rhizoryzae	strain=DK36	GCA_008629685.1	2607907	2607907	type	True	84.8778	1490	2179	95	below_threshold
Adhaeribacter swui	strain=KCTC 52873	GCA_014217805.1	2086471	2086471	type	True	77.3411	409	2179	95	below_threshold
Adhaeribacter aquaticus	strain=DSM 16391	GCA_000473365.1	299567	299567	type	True	77.3035	324	2179	95	below_threshold
Adhaeribacter radiodurans	strain=KUDC8001	GCA_014075995.1	2745197	2745197	type	True	77.0882	342	2179	95	below_threshold
Adhaeribacter pallidiroseus	strain=HMF7616	GCA_003340495.1	2072847	2072847	type	True	76.9911	358	2179	95	below_threshold
Adhaeribacter arboris	strain=HMF7605	GCA_003023845.1	2072846	2072846	type	True	76.8481	357	2179	95	below_threshold
Adhaeribacter soli	strain=MA2	GCA_008727925.1	2607655	2607655	type	True	76.671	209	2179	95	below_threshold
Pontibacter ruber	strain=JC213	GCA_023630205.1	1343895	1343895	type	True	76.3817	88	2179	95	below_threshold
Pontibacter arcticus	strain=2b14	GCA_003284895.1	2080288	2080288	type	True	76.2932	124	2179	95	below_threshold
Rufibacter sediminis	strain=CGMCC 1.16289	GCA_024436355.1	2762756	2762756	type	True	76.2836	119	2179	95	below_threshold
Rufibacter latericius	strain=R-22-1 c-1	GCA_003721515.1	2487040	2487040	type	True	76.1302	116	2179	95	below_threshold
Pontibacter silvestris	strain=XAAS-R86T	GCA_020907275.1	2305183	2305183	type	True	75.9624	73	2179	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:39,762] [INFO] DFAST Taxonomy check result was written to GCF_007991635.1_ASM799163v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:39,763] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:39,763] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:39,763] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0b765ddf-35d1-4021-916e-fff16a215cdd/dqc_reference/checkm_data
[2024-01-24 11:59:39,764] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:39,829] [INFO] Task started: CheckM
[2024-01-24 11:59:39,829] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007991635.1_ASM799163v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007991635.1_ASM799163v1_genomic.fna/checkm_input GCF_007991635.1_ASM799163v1_genomic.fna/checkm_result
[2024-01-24 12:00:45,528] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:45,529] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:45,544] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:45,545] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:45,545] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007991635.1_ASM799163v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:45,545] [INFO] Task started: Blastn
[2024-01-24 12:00:45,545] [INFO] Running command: blastn -query GCF_007991635.1_ASM799163v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b765ddf-35d1-4021-916e-fff16a215cdd/dqc_reference/reference_markers_gtdb.fasta -out GCF_007991635.1_ASM799163v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:46,331] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:46,335] [INFO] Selected 12 target genomes.
[2024-01-24 12:00:46,335] [INFO] Target genome list was writen to GCF_007991635.1_ASM799163v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:46,342] [INFO] Task started: fastANI
[2024-01-24 12:00:46,342] [INFO] Running command: fastANI --query /var/lib/cwl/stg977cfc17-82e6-4f00-a831-a170045d6f2e/GCF_007991635.1_ASM799163v1_genomic.fna.gz --refList GCF_007991635.1_ASM799163v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007991635.1_ASM799163v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:58,504] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:58,513] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:58,513] [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_007991635.1	s__Adhaeribacter aerolatus	100.0	2174	2179	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_008629685.1	s__Adhaeribacter rhizoryzae	84.8798	1490	2179	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	77.321	412	2179	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	77.3035	324	2179	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Adhaeribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014075995.1	s__Adhaeribacter radiodurans	77.0807	343	2179	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	76.9846	359	2179	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Adhaeribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003023845.1	s__Adhaeribacter arboris	76.848	357	2179	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	76.671	209	2179	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Adhaeribacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001577755.1	s__Nibribacter sp001577755	76.5671	71	2179	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Nibribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003721515.1	s__Rufibacter latericius	76.1302	116	2179	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Rufibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:58,514] [INFO] GTDB search result was written to GCF_007991635.1_ASM799163v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:58,515] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:58,518] [INFO] DFAST_QC result json was written to GCF_007991635.1_ASM799163v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:58,518] [INFO] DFAST_QC completed!
[2024-01-24 12:00:58,518] [INFO] Total running time: 0h2m1s