[2024-01-24 14:56:23,787] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:56:23,789] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:56:23,790] [INFO] DQC Reference Directory: /var/lib/cwl/stg27d79e00-f03a-4bd8-a332-cdeda1e450ec/dqc_reference
[2024-01-24 14:56:26,558] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:56:26,559] [INFO] Task started: Prodigal
[2024-01-24 14:56:26,560] [INFO] Running command: gunzip -c /var/lib/cwl/stge4d635ea-5171-4cd4-9b58-da6d6793b875/GCF_004349265.1_ASM434926v1_genomic.fna.gz | prodigal -d GCF_004349265.1_ASM434926v1_genomic.fna/cds.fna -a GCF_004349265.1_ASM434926v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:57:02,973] [INFO] Task succeeded: Prodigal
[2024-01-24 14:57:02,973] [INFO] Task started: HMMsearch
[2024-01-24 14:57:02,974] [INFO] Running command: hmmsearch --tblout GCF_004349265.1_ASM434926v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg27d79e00-f03a-4bd8-a332-cdeda1e450ec/dqc_reference/reference_markers.hmm GCF_004349265.1_ASM434926v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:57:03,476] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:57:03,478] [INFO] Found 6/6 markers.
[2024-01-24 14:57:03,547] [INFO] Query marker FASTA was written to GCF_004349265.1_ASM434926v1_genomic.fna/markers.fasta
[2024-01-24 14:57:03,547] [INFO] Task started: Blastn
[2024-01-24 14:57:03,548] [INFO] Running command: blastn -query GCF_004349265.1_ASM434926v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg27d79e00-f03a-4bd8-a332-cdeda1e450ec/dqc_reference/reference_markers.fasta -out GCF_004349265.1_ASM434926v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:57:04,207] [INFO] Task succeeded: Blastn
[2024-01-24 14:57:04,212] [INFO] Selected 20 target genomes.
[2024-01-24 14:57:04,212] [INFO] Target genome list was writen to GCF_004349265.1_ASM434926v1_genomic.fna/target_genomes.txt
[2024-01-24 14:57:04,251] [INFO] Task started: fastANI
[2024-01-24 14:57:04,251] [INFO] Running command: fastANI --query /var/lib/cwl/stge4d635ea-5171-4cd4-9b58-da6d6793b875/GCF_004349265.1_ASM434926v1_genomic.fna.gz --refList GCF_004349265.1_ASM434926v1_genomic.fna/target_genomes.txt --output GCF_004349265.1_ASM434926v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:57:26,561] [INFO] Task succeeded: fastANI
[2024-01-24 14:57:26,562] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg27d79e00-f03a-4bd8-a332-cdeda1e450ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:57:26,563] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg27d79e00-f03a-4bd8-a332-cdeda1e450ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:57:26,577] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:57:26,577] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:57:26,578] [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 psychrotolerans	strain=AR-3-6	GCA_004349265.1	2541721	2541721	type	True	100.0	2612	2617	95	conclusive
Dyadobacter psychrophilus	strain=DSM 22270	GCA_900167945.1	651661	651661	type	True	79.0031	437	2617	95	below_threshold
Dyadobacter frigoris	strain=AR-3-8	GCA_005280585.1	2576211	2576211	type	True	78.8763	521	2617	95	below_threshold
Dyadobacter flavalbus	strain=NS28	GCA_006149045.1	2579942	2579942	type	True	78.6501	442	2617	95	below_threshold
Dyadobacter sediminis	strain=CGMCC 1.12895	GCA_014640015.1	1493691	1493691	type	True	78.5485	409	2617	95	below_threshold
Dyadobacter luteus	strain=RS19	GCA_003383615.1	2259619	2259619	type	True	78.4141	538	2617	95	below_threshold
Dyadobacter koreensis	strain=DSM 19938	GCA_900108855.1	408657	408657	type	True	78.3501	460	2617	95	below_threshold
Dyadobacter subterraneus	strain=UP-52	GCA_015221875.1	2773304	2773304	type	True	78.0453	523	2617	95	below_threshold
Dyadobacter alkalitolerans	strain=DSM 23607	GCA_000428845.1	492736	492736	type	True	77.8277	380	2617	95	below_threshold
Dyadobacter arcticus	strain=DSM 102865	GCA_011762185.1	1078754	1078754	type	True	77.4625	287	2617	95	below_threshold
Dyadobacter endophyticus	strain=CGMCC 1.15288	GCA_014641595.1	1749036	1749036	type	True	77.0426	308	2617	95	below_threshold
Dyadobacter jiangsuensis	strain=DSM 29057	GCA_003014695.1	1591085	1591085	type	True	76.9738	300	2617	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:57:26,579] [INFO] DFAST Taxonomy check result was written to GCF_004349265.1_ASM434926v1_genomic.fna/tc_result.tsv
[2024-01-24 14:57:26,580] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:57:26,580] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:57:26,580] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg27d79e00-f03a-4bd8-a332-cdeda1e450ec/dqc_reference/checkm_data
[2024-01-24 14:57:26,581] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:57:26,656] [INFO] Task started: CheckM
[2024-01-24 14:57:26,657] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004349265.1_ASM434926v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004349265.1_ASM434926v1_genomic.fna/checkm_input GCF_004349265.1_ASM434926v1_genomic.fna/checkm_result
[2024-01-24 14:59:03,150] [INFO] Task succeeded: CheckM
[2024-01-24 14:59:03,151] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:59:03,176] [INFO] ===== Completeness check finished =====
[2024-01-24 14:59:03,177] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:59:03,177] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004349265.1_ASM434926v1_genomic.fna/markers.fasta)
[2024-01-24 14:59:03,177] [INFO] Task started: Blastn
[2024-01-24 14:59:03,178] [INFO] Running command: blastn -query GCF_004349265.1_ASM434926v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg27d79e00-f03a-4bd8-a332-cdeda1e450ec/dqc_reference/reference_markers_gtdb.fasta -out GCF_004349265.1_ASM434926v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:59:03,997] [INFO] Task succeeded: Blastn
[2024-01-24 14:59:04,002] [INFO] Selected 19 target genomes.
[2024-01-24 14:59:04,002] [INFO] Target genome list was writen to GCF_004349265.1_ASM434926v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:59:04,024] [INFO] Task started: fastANI
[2024-01-24 14:59:04,024] [INFO] Running command: fastANI --query /var/lib/cwl/stge4d635ea-5171-4cd4-9b58-da6d6793b875/GCF_004349265.1_ASM434926v1_genomic.fna.gz --refList GCF_004349265.1_ASM434926v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004349265.1_ASM434926v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:59:24,939] [INFO] Task succeeded: fastANI
[2024-01-24 14:59:24,957] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:59:24,957] [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_004349265.1	s__Dyadobacter psychrotolerans	100.0	2612	2617	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	79.0031	437	2617	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	78.8697	520	2617	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	78.6678	413	2617	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	78.636	444	2617	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003383615.1	s__Dyadobacter luteus	78.4185	538	2617	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108855.1	s__Dyadobacter koreensis	78.3501	460	2617	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	78.0205	520	2617	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	77.9032	495	2617	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	77.8051	380	2617	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	77.6586	342	2617	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	77.4528	288	2617	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003014695.1	s__Dyadobacter jiangsuensis	76.9734	299	2617	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009296315.1	s__Persicitalea sp009296315	76.397	73	2617	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Persicitalea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:59:24,959] [INFO] GTDB search result was written to GCF_004349265.1_ASM434926v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:59:24,959] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:59:24,963] [INFO] DFAST_QC result json was written to GCF_004349265.1_ASM434926v1_genomic.fna/dqc_result.json
[2024-01-24 14:59:24,963] [INFO] DFAST_QC completed!
[2024-01-24 14:59:24,963] [INFO] Total running time: 0h3m1s