[2024-01-24 14:55:34,432] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:34,434] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:34,434] [INFO] DQC Reference Directory: /var/lib/cwl/stgf9a8df58-afac-49ae-b1c3-ca11d78d03d5/dqc_reference
[2024-01-24 14:55:35,675] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:35,676] [INFO] Task started: Prodigal
[2024-01-24 14:55:35,676] [INFO] Running command: gunzip -c /var/lib/cwl/stg571b1694-c8ce-404c-b0bd-7adef9619e46/GCF_005860805.1_ASM586080v1_genomic.fna.gz | prodigal -d GCF_005860805.1_ASM586080v1_genomic.fna/cds.fna -a GCF_005860805.1_ASM586080v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:56:09,616] [INFO] Task succeeded: Prodigal
[2024-01-24 14:56:09,616] [INFO] Task started: HMMsearch
[2024-01-24 14:56:09,616] [INFO] Running command: hmmsearch --tblout GCF_005860805.1_ASM586080v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf9a8df58-afac-49ae-b1c3-ca11d78d03d5/dqc_reference/reference_markers.hmm GCF_005860805.1_ASM586080v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:56:09,965] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:56:09,967] [INFO] Found 6/6 markers.
[2024-01-24 14:56:10,020] [INFO] Query marker FASTA was written to GCF_005860805.1_ASM586080v1_genomic.fna/markers.fasta
[2024-01-24 14:56:10,020] [INFO] Task started: Blastn
[2024-01-24 14:56:10,020] [INFO] Running command: blastn -query GCF_005860805.1_ASM586080v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9a8df58-afac-49ae-b1c3-ca11d78d03d5/dqc_reference/reference_markers.fasta -out GCF_005860805.1_ASM586080v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:10,667] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:10,671] [INFO] Selected 19 target genomes.
[2024-01-24 14:56:10,672] [INFO] Target genome list was writen to GCF_005860805.1_ASM586080v1_genomic.fna/target_genomes.txt
[2024-01-24 14:56:10,680] [INFO] Task started: fastANI
[2024-01-24 14:56:10,681] [INFO] Running command: fastANI --query /var/lib/cwl/stg571b1694-c8ce-404c-b0bd-7adef9619e46/GCF_005860805.1_ASM586080v1_genomic.fna.gz --refList GCF_005860805.1_ASM586080v1_genomic.fna/target_genomes.txt --output GCF_005860805.1_ASM586080v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:56:35,647] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:35,648] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf9a8df58-afac-49ae-b1c3-ca11d78d03d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:56:35,649] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf9a8df58-afac-49ae-b1c3-ca11d78d03d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:56:35,665] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:56:35,665] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:56:35,665] [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 luticola	strain=T17	GCA_005860805.1	1979387	1979387	type	True	100.0	2130	2130	95	conclusive
Dyadobacter psychrophilus	strain=DSM 22270	GCA_900167945.1	651661	651661	type	True	78.5696	694	2130	95	below_threshold
Dyadobacter alkalitolerans	strain=DSM 23607	GCA_000428845.1	492736	492736	type	True	78.4529	669	2130	95	below_threshold
Dyadobacter soli	strain=DSM 25329	GCA_900101885.1	659014	659014	type	True	78.3018	749	2130	95	below_threshold
Dyadobacter sandarakinus	strain=Q3-56	GCA_016894445.1	2747268	2747268	type	True	78.252	557	2130	95	below_threshold
Dyadobacter beijingensis	strain=CGMCC 1.6375	GCA_014645155.1	365489	365489	type	True	78.2357	742	2130	95	below_threshold
Dyadobacter beijingensis	strain=DSM 21582	GCA_000382205.1	365489	365489	type	True	78.2143	745	2130	95	below_threshold
Dyadobacter crusticola	strain=DSM 16708	GCA_000701505.1	292407	292407	type	True	78.2008	655	2130	95	below_threshold
Dyadobacter fermentans	strain=DSM 18053	GCA_000023125.1	94254	94254	type	True	78.1225	669	2130	95	below_threshold
Dyadobacter endophyticus	strain=CGMCC 1.15288	GCA_014641595.1	1749036	1749036	type	True	78.1203	660	2130	95	below_threshold
Dyadobacter jiangsuensis	strain=DSM 29057	GCA_003014695.1	1591085	1591085	type	True	78.0254	688	2130	95	below_threshold
Dyadobacter flavalbus	strain=NS28	GCA_006149045.1	2579942	2579942	type	True	77.9922	535	2130	95	below_threshold
Dyadobacter sediminis	strain=CGMCC 1.12895	GCA_014640015.1	1493691	1493691	type	True	77.8438	544	2130	95	below_threshold
Dyadobacter sediminis	strain=Z12	GCA_005860765.1	1493691	1493691	type	True	77.8113	551	2130	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:56:35,684] [INFO] DFAST Taxonomy check result was written to GCF_005860805.1_ASM586080v1_genomic.fna/tc_result.tsv
[2024-01-24 14:56:35,685] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:56:35,686] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:56:35,686] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf9a8df58-afac-49ae-b1c3-ca11d78d03d5/dqc_reference/checkm_data
[2024-01-24 14:56:35,688] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:56:35,749] [INFO] Task started: CheckM
[2024-01-24 14:56:35,749] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005860805.1_ASM586080v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005860805.1_ASM586080v1_genomic.fna/checkm_input GCF_005860805.1_ASM586080v1_genomic.fna/checkm_result
[2024-01-24 14:58:07,683] [INFO] Task succeeded: CheckM
[2024-01-24 14:58:07,685] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:58:07,707] [INFO] ===== Completeness check finished =====
[2024-01-24 14:58:07,708] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:58:07,708] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005860805.1_ASM586080v1_genomic.fna/markers.fasta)
[2024-01-24 14:58:07,708] [INFO] Task started: Blastn
[2024-01-24 14:58:07,708] [INFO] Running command: blastn -query GCF_005860805.1_ASM586080v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9a8df58-afac-49ae-b1c3-ca11d78d03d5/dqc_reference/reference_markers_gtdb.fasta -out GCF_005860805.1_ASM586080v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:58:08,576] [INFO] Task succeeded: Blastn
[2024-01-24 14:58:08,580] [INFO] Selected 19 target genomes.
[2024-01-24 14:58:08,580] [INFO] Target genome list was writen to GCF_005860805.1_ASM586080v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:58:08,595] [INFO] Task started: fastANI
[2024-01-24 14:58:08,595] [INFO] Running command: fastANI --query /var/lib/cwl/stg571b1694-c8ce-404c-b0bd-7adef9619e46/GCF_005860805.1_ASM586080v1_genomic.fna.gz --refList GCF_005860805.1_ASM586080v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005860805.1_ASM586080v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:58:31,555] [INFO] Task succeeded: fastANI
[2024-01-24 14:58:31,575] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:58:31,575] [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_005860805.1	s__Dyadobacter luticola	100.0	2130	2130	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_011762185.1	s__Dyadobacter arcticus	78.718	758	2130	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167945.1	s__Dyadobacter psychrophilus	78.5708	693	2130	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	78.5442	666	2130	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	78.4738	706	2130	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	78.3443	642	2130	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101885.1	s__Dyadobacter soli	78.3083	747	2130	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	78.2514	557	2130	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382205.1	s__Dyadobacter beijingensis	78.2073	745	2130	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000701505.1	s__Dyadobacter crusticola	78.1992	656	2130	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898145.1	s__Dyadobacter sp001898145	78.1555	645	2130	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	99.32	99.32	0.98	0.98	2	-
GCF_000023125.1	s__Dyadobacter fermentans	78.122	666	2130	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	78.1167	661	2130	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109045.1	s__Dyadobacter sp900109045	78.1016	723	2130	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	78.0144	689	2130	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006149045.1	s__Dyadobacter flavalbus	77.9986	534	2130	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	77.8113	551	2130	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:58:31,577] [INFO] GTDB search result was written to GCF_005860805.1_ASM586080v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:58:31,585] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:58:31,592] [INFO] DFAST_QC result json was written to GCF_005860805.1_ASM586080v1_genomic.fna/dqc_result.json
[2024-01-24 14:58:31,593] [INFO] DFAST_QC completed!
[2024-01-24 14:58:31,593] [INFO] Total running time: 0h2m57s