[2024-01-24 15:06:36,797] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:06:36,798] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:06:36,799] [INFO] DQC Reference Directory: /var/lib/cwl/stg571673c1-76f1-4994-bb4f-f9b39adf79de/dqc_reference
[2024-01-24 15:06:38,255] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:06:38,256] [INFO] Task started: Prodigal
[2024-01-24 15:06:38,257] [INFO] Running command: gunzip -c /var/lib/cwl/stg4357030d-5bf9-4fea-ba4f-d01f016dc4d9/GCF_005869225.1_ASM586922v1_genomic.fna.gz | prodigal -d GCF_005869225.1_ASM586922v1_genomic.fna/cds.fna -a GCF_005869225.1_ASM586922v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:07:21,545] [INFO] Task succeeded: Prodigal
[2024-01-24 15:07:21,546] [INFO] Task started: HMMsearch
[2024-01-24 15:07:21,546] [INFO] Running command: hmmsearch --tblout GCF_005869225.1_ASM586922v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg571673c1-76f1-4994-bb4f-f9b39adf79de/dqc_reference/reference_markers.hmm GCF_005869225.1_ASM586922v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:07:21,960] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:07:21,961] [INFO] Found 6/6 markers.
[2024-01-24 15:07:22,070] [INFO] Query marker FASTA was written to GCF_005869225.1_ASM586922v1_genomic.fna/markers.fasta
[2024-01-24 15:07:22,070] [INFO] Task started: Blastn
[2024-01-24 15:07:22,070] [INFO] Running command: blastn -query GCF_005869225.1_ASM586922v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg571673c1-76f1-4994-bb4f-f9b39adf79de/dqc_reference/reference_markers.fasta -out GCF_005869225.1_ASM586922v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:07:22,698] [INFO] Task succeeded: Blastn
[2024-01-24 15:07:22,702] [INFO] Selected 22 target genomes.
[2024-01-24 15:07:22,703] [INFO] Target genome list was writen to GCF_005869225.1_ASM586922v1_genomic.fna/target_genomes.txt
[2024-01-24 15:07:22,717] [INFO] Task started: fastANI
[2024-01-24 15:07:22,717] [INFO] Running command: fastANI --query /var/lib/cwl/stg4357030d-5bf9-4fea-ba4f-d01f016dc4d9/GCF_005869225.1_ASM586922v1_genomic.fna.gz --refList GCF_005869225.1_ASM586922v1_genomic.fna/target_genomes.txt --output GCF_005869225.1_ASM586922v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:07:47,162] [INFO] Task succeeded: fastANI
[2024-01-24 15:07:47,163] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg571673c1-76f1-4994-bb4f-f9b39adf79de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:07:47,164] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg571673c1-76f1-4994-bb4f-f9b39adf79de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:07:47,182] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:07:47,182] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:07:47,183] [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
Dyadobacter bucti	strain=QTA69	GCA_005869225.1	2572203	2572203	type	True	100.0	2786	2786	95	conclusive
Dyadobacter psychrophilus	strain=DSM 22270	GCA_900167945.1	651661	651661	type	True	79.2567	680	2786	95	below_threshold
Dyadobacter sediminis	strain=Z12	GCA_005860765.1	1493691	1493691	type	True	79.0576	614	2786	95	below_threshold
Dyadobacter sediminis	strain=CGMCC 1.12895	GCA_014640015.1	1493691	1493691	type	True	79.0212	614	2786	95	below_threshold
Dyadobacter flavalbus	strain=NS28	GCA_006149045.1	2579942	2579942	type	True	78.7857	627	2786	95	below_threshold
Dyadobacter alkalitolerans	strain=DSM 23607	GCA_000428845.1	492736	492736	type	True	78.7263	621	2786	95	below_threshold
Dyadobacter luticola	strain=T17	GCA_005860805.1	1979387	1979387	type	True	78.4104	582	2786	95	below_threshold
Dyadobacter arcticus	strain=DSM 102865	GCA_011762185.1	1078754	1078754	type	True	78.0872	452	2786	95	below_threshold
Dyadobacter endophyticus	strain=CGMCC 1.15288	GCA_014641595.1	1749036	1749036	type	True	77.8593	552	2786	95	below_threshold
Dyadobacter crusticola	strain=DSM 16708	GCA_000701505.1	292407	292407	type	True	77.7965	477	2786	95	below_threshold
Dyadobacter sandarakinus	strain=Q3-56	GCA_016894445.1	2747268	2747268	type	True	77.5887	445	2786	95	below_threshold
Dyadobacter frigoris	strain=AR-3-8	GCA_005280585.1	2576211	2576211	type	True	77.5297	346	2786	95	below_threshold
Dyadobacter beijingensis	strain=DSM 21582	GCA_000382205.1	365489	365489	type	True	77.4982	527	2786	95	below_threshold
Dyadobacter subterraneus	strain=UP-52	GCA_015221875.1	2773304	2773304	type	True	77.3782	374	2786	95	below_threshold
Arundinibacter roseus	strain=DMA-K-7a	GCA_004348825.1	2070510	2070510	type	True	76.2248	93	2786	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:07:47,185] [INFO] DFAST Taxonomy check result was written to GCF_005869225.1_ASM586922v1_genomic.fna/tc_result.tsv
[2024-01-24 15:07:47,185] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:07:47,185] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:07:47,186] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg571673c1-76f1-4994-bb4f-f9b39adf79de/dqc_reference/checkm_data
[2024-01-24 15:07:47,187] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:07:47,261] [INFO] Task started: CheckM
[2024-01-24 15:07:47,261] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005869225.1_ASM586922v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005869225.1_ASM586922v1_genomic.fna/checkm_input GCF_005869225.1_ASM586922v1_genomic.fna/checkm_result
[2024-01-24 15:09:37,986] [INFO] Task succeeded: CheckM
[2024-01-24 15:09:37,988] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:09:38,014] [INFO] ===== Completeness check finished =====
[2024-01-24 15:09:38,015] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:09:38,015] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005869225.1_ASM586922v1_genomic.fna/markers.fasta)
[2024-01-24 15:09:38,016] [INFO] Task started: Blastn
[2024-01-24 15:09:38,016] [INFO] Running command: blastn -query GCF_005869225.1_ASM586922v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg571673c1-76f1-4994-bb4f-f9b39adf79de/dqc_reference/reference_markers_gtdb.fasta -out GCF_005869225.1_ASM586922v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:09:38,802] [INFO] Task succeeded: Blastn
[2024-01-24 15:09:38,806] [INFO] Selected 21 target genomes.
[2024-01-24 15:09:38,807] [INFO] Target genome list was writen to GCF_005869225.1_ASM586922v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:09:38,854] [INFO] Task started: fastANI
[2024-01-24 15:09:38,854] [INFO] Running command: fastANI --query /var/lib/cwl/stg4357030d-5bf9-4fea-ba4f-d01f016dc4d9/GCF_005869225.1_ASM586922v1_genomic.fna.gz --refList GCF_005869225.1_ASM586922v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005869225.1_ASM586922v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:10:03,626] [INFO] Task succeeded: fastANI
[2024-01-24 15:10:03,645] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:10:03,645] [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_005869225.1	s__Dyadobacter bucti	100.0	2786	2786	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900167945.1	s__Dyadobacter psychrophilus	79.2563	681	2786	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005860765.1	s__Dyadobacter sediminis	79.0576	614	2786	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006149045.1	s__Dyadobacter flavalbus	78.7857	627	2786	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000428845.1	s__Dyadobacter alkalitolerans	78.7202	620	2786	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005860805.1	s__Dyadobacter luticola	78.417	581	2786	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_907165045.1	s__Dyadobacter sp907165045	78.1645	551	2786	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008369915.1	s__Dyadobacter sp008369915	78.1479	551	2786	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011762185.1	s__Dyadobacter arcticus	78.0952	451	2786	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424405.1	s__Dyadobacter sp001424405	77.8802	503	2786	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641595.1	s__Dyadobacter endophyticus	77.8656	551	2786	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000701505.1	s__Dyadobacter crusticola	77.7965	477	2786	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016894445.1	s__Dyadobacter sp016894445	77.5853	445	2786	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_907164905.1	s__Dyadobacter sp907164905	77.559	395	2786	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005280585.1	s__Dyadobacter frigoris	77.5206	347	2786	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015221875.1	s__Dyadobacter sp015221875	77.3655	373	2786	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009801115.1	s__Dyadobacter sp009801115	77.2992	361	2786	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348825.1	s__Arundinibacter roseus	76.2248	93	2786	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Arundinibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:10:03,647] [INFO] GTDB search result was written to GCF_005869225.1_ASM586922v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:10:03,647] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:10:03,651] [INFO] DFAST_QC result json was written to GCF_005869225.1_ASM586922v1_genomic.fna/dqc_result.json
[2024-01-24 15:10:03,651] [INFO] DFAST_QC completed!
[2024-01-24 15:10:03,651] [INFO] Total running time: 0h3m27s