[2024-01-24 13:37:27,971] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:27,973] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:27,973] [INFO] DQC Reference Directory: /var/lib/cwl/stgbc47605b-915e-466d-8cc4-203e1fbcf021/dqc_reference
[2024-01-24 13:37:29,283] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:29,284] [INFO] Task started: Prodigal
[2024-01-24 13:37:29,285] [INFO] Running command: gunzip -c /var/lib/cwl/stgc794a330-6e49-4bb5-9e84-447dae252ade/GCF_021568775.1_ASM2156877v1_genomic.fna.gz | prodigal -d GCF_021568775.1_ASM2156877v1_genomic.fna/cds.fna -a GCF_021568775.1_ASM2156877v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:42,921] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:42,921] [INFO] Task started: HMMsearch
[2024-01-24 13:37:42,921] [INFO] Running command: hmmsearch --tblout GCF_021568775.1_ASM2156877v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbc47605b-915e-466d-8cc4-203e1fbcf021/dqc_reference/reference_markers.hmm GCF_021568775.1_ASM2156877v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:43,240] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:43,241] [INFO] Found 6/6 markers.
[2024-01-24 13:37:43,283] [INFO] Query marker FASTA was written to GCF_021568775.1_ASM2156877v1_genomic.fna/markers.fasta
[2024-01-24 13:37:43,284] [INFO] Task started: Blastn
[2024-01-24 13:37:43,284] [INFO] Running command: blastn -query GCF_021568775.1_ASM2156877v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc47605b-915e-466d-8cc4-203e1fbcf021/dqc_reference/reference_markers.fasta -out GCF_021568775.1_ASM2156877v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:44,617] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:44,620] [INFO] Selected 21 target genomes.
[2024-01-24 13:37:44,621] [INFO] Target genome list was writen to GCF_021568775.1_ASM2156877v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:44,632] [INFO] Task started: fastANI
[2024-01-24 13:37:44,632] [INFO] Running command: fastANI --query /var/lib/cwl/stgc794a330-6e49-4bb5-9e84-447dae252ade/GCF_021568775.1_ASM2156877v1_genomic.fna.gz --refList GCF_021568775.1_ASM2156877v1_genomic.fna/target_genomes.txt --output GCF_021568775.1_ASM2156877v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:38:03,664] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:03,665] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbc47605b-915e-466d-8cc4-203e1fbcf021/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:38:03,665] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbc47605b-915e-466d-8cc4-203e1fbcf021/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:38:03,683] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:38:03,683] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:38:03,684] [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
Promicromonospora citrea	strain=ATCC 15908	GCA_013004695.1	43677	43677	type	True	80.8235	762	1648	95	below_threshold
Promicromonospora citrea	strain=JCM 3051	GCA_014647735.1	43677	43677	type	True	80.7975	808	1648	95	below_threshold
Promicromonospora sukumoe	strain=DSM 44121	GCA_014137995.1	88382	88382	type	True	80.7495	880	1648	95	below_threshold
Promicromonospora kroppenstedtii	strain=DSM 19349	GCA_000515355.1	440482	440482	type	True	80.5484	815	1648	95	below_threshold
Promicromonospora umidemergens	strain=DSM 22081	GCA_024171995.1	629679	629679	type	True	80.3663	843	1648	95	below_threshold
Myceligenerans xiligouense	strain=DSM 15700	GCA_003814695.1	253184	253184	type	True	80.3473	724	1648	95	below_threshold
Myceligenerans indicum	strain=I2	GCA_016742955.1	2593663	2593663	type	True	79.8977	676	1648	95	below_threshold
Cellulosimicrobium marinum	strain=NBRC 110994	GCA_020551945.1	1638992	1638992	type	True	79.8049	649	1648	95	below_threshold
Cellulosimicrobium funkei	strain=NBRC 104118	GCA_001570825.1	264251	264251	suspected-type	True	79.7376	698	1648	95	below_threshold
Cellulosimicrobium funkei	strain=JCM 14302	GCA_004519295.1	264251	264251	suspected-type	True	79.7354	711	1648	95	below_threshold
Myceligenerans salitolerans	strain=XHU 5031	GCA_017349295.1	1230528	1230528	type	True	79.6714	673	1648	95	below_threshold
Sediminihabitans luteus	strain=DSM 25478	GCA_002797595.1	1138585	1138585	type	True	79.5276	605	1648	95	below_threshold
Sediminihabitans luteus	strain=NBRC 108568	GCA_016863455.1	1138585	1138585	type	True	79.4748	606	1648	95	below_threshold
Isoptericola sediminis	strain=JC619	GCA_013085345.1	2733572	2733572	type	True	79.3629	544	1648	95	below_threshold
Isoptericola chiayiensis	strain=KCTC 19740	GCA_013149805.1	579446	579446	type	True	79.3493	604	1648	95	below_threshold
Cellulomonas biazotea	strain=NBRC12680	GCA_004306155.1	1709	1709	type	True	78.9575	544	1648	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	78.7516	577	1648	95	below_threshold
Cellulomonas gilvus	strain=ATCC 13127	GCA_000218545.1	11	11	type	True	78.5178	504	1648	95	below_threshold
Cellulomonas fulva	strain=DKR-3	GCA_018531375.1	2835530	2835530	type	True	78.4066	546	1648	95	below_threshold
Cellulomonas avistercoris	strain=Sa3CUA2	GCA_014836445.1	2762242	2762242	type	True	78.3005	537	1648	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	78.2554	573	1648	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:38:03,685] [INFO] DFAST Taxonomy check result was written to GCF_021568775.1_ASM2156877v1_genomic.fna/tc_result.tsv
[2024-01-24 13:38:03,686] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:38:03,686] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:38:03,686] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbc47605b-915e-466d-8cc4-203e1fbcf021/dqc_reference/checkm_data
[2024-01-24 13:38:03,688] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:38:03,736] [INFO] Task started: CheckM
[2024-01-24 13:38:03,737] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021568775.1_ASM2156877v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021568775.1_ASM2156877v1_genomic.fna/checkm_input GCF_021568775.1_ASM2156877v1_genomic.fna/checkm_result
[2024-01-24 13:38:54,238] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:54,239] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:54,294] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:54,295] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:54,295] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021568775.1_ASM2156877v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:54,296] [INFO] Task started: Blastn
[2024-01-24 13:38:54,296] [INFO] Running command: blastn -query GCF_021568775.1_ASM2156877v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc47605b-915e-466d-8cc4-203e1fbcf021/dqc_reference/reference_markers_gtdb.fasta -out GCF_021568775.1_ASM2156877v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:56,344] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:56,350] [INFO] Selected 18 target genomes.
[2024-01-24 13:38:56,350] [INFO] Target genome list was writen to GCF_021568775.1_ASM2156877v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:56,638] [INFO] Task started: fastANI
[2024-01-24 13:38:56,638] [INFO] Running command: fastANI --query /var/lib/cwl/stgc794a330-6e49-4bb5-9e84-447dae252ade/GCF_021568775.1_ASM2156877v1_genomic.fna.gz --refList GCF_021568775.1_ASM2156877v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021568775.1_ASM2156877v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:39:15,331] [INFO] Task succeeded: fastANI
[2024-01-24 13:39:15,350] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:39:15,350] [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_003946865.1	s__Antribacter gilvus	82.559	985	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Antribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003058225.1	s__Promicromonospora sp003058225	81.5302	961	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	98.27	98.27	0.94	0.94	2	-
GCA_009663185.1	s__Isoptericola sp009663185	81.2505	767	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000215105.1	s__Isoptericola variabilis_A	80.9266	698	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	99.96	99.96	0.98	0.98	2	-
GCF_003096495.1	s__Promicromonospora sukumoe_A	80.9172	880	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013004695.1	s__Promicromonospora citrea	80.8623	757	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	99.97	99.97	0.99	0.99	2	-
GCF_014137995.1	s__Promicromonospora sukumoe	80.7679	877	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003550025.1	s__Promicromonospora thailandica	80.7069	885	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000385135.1	s__Promicromonospora sukumoe_B	80.6778	901	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	95.99	95.99	0.93	0.93	2	-
GCF_000515355.1	s__Promicromonospora kroppenstedtii	80.54	817	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	97.09	97.09	0.84	0.84	2	-
GCF_001750215.1	s__Xylanimonas variabilis_A	80.5357	522	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Xylanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009846865.1	s__Xylanimonas puerhi	80.1798	664	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Xylanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009783295.1	s__Xylanimonas sp009783295	79.9432	587	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Xylanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016742955.1	s__Myceligenerans indicum	79.8816	678	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Myceligenerans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167525.1	s__Isoptericola flava	79.7515	741	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004519295.1	s__Cellulosimicrobium funkei	79.7385	711	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	96.0261	98.03	96.84	0.93	0.88	18	-
GCF_011634835.1	s__Isoptericola sp011634835	79.5852	711	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013149805.1	s__Isoptericola chiayiensis	79.3443	604	1648	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:39:15,352] [INFO] GTDB search result was written to GCF_021568775.1_ASM2156877v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:39:15,352] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:39:15,379] [INFO] DFAST_QC result json was written to GCF_021568775.1_ASM2156877v1_genomic.fna/dqc_result.json
[2024-01-24 13:39:15,380] [INFO] DFAST_QC completed!
[2024-01-24 13:39:15,380] [INFO] Total running time: 0h1m47s