[2024-01-24 10:57:05,453] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:05,455] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:05,455] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e49e14a-0236-42c5-bd27-390bf778a02d/dqc_reference
[2024-01-24 10:57:06,751] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:06,752] [INFO] Task started: Prodigal
[2024-01-24 10:57:06,752] [INFO] Running command: gunzip -c /var/lib/cwl/stg9cd0d116-b0df-4900-9f55-bc7f2d726597/GCF_004216535.1_ASM421653v1_genomic.fna.gz | prodigal -d GCF_004216535.1_ASM421653v1_genomic.fna/cds.fna -a GCF_004216535.1_ASM421653v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:18,119] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:18,120] [INFO] Task started: HMMsearch
[2024-01-24 10:57:18,120] [INFO] Running command: hmmsearch --tblout GCF_004216535.1_ASM421653v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e49e14a-0236-42c5-bd27-390bf778a02d/dqc_reference/reference_markers.hmm GCF_004216535.1_ASM421653v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:18,389] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:18,390] [INFO] Found 6/6 markers.
[2024-01-24 10:57:18,428] [INFO] Query marker FASTA was written to GCF_004216535.1_ASM421653v1_genomic.fna/markers.fasta
[2024-01-24 10:57:18,428] [INFO] Task started: Blastn
[2024-01-24 10:57:18,429] [INFO] Running command: blastn -query GCF_004216535.1_ASM421653v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e49e14a-0236-42c5-bd27-390bf778a02d/dqc_reference/reference_markers.fasta -out GCF_004216535.1_ASM421653v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:19,760] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:19,764] [INFO] Selected 26 target genomes.
[2024-01-24 10:57:19,765] [INFO] Target genome list was writen to GCF_004216535.1_ASM421653v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:19,776] [INFO] Task started: fastANI
[2024-01-24 10:57:19,776] [INFO] Running command: fastANI --query /var/lib/cwl/stg9cd0d116-b0df-4900-9f55-bc7f2d726597/GCF_004216535.1_ASM421653v1_genomic.fna.gz --refList GCF_004216535.1_ASM421653v1_genomic.fna/target_genomes.txt --output GCF_004216535.1_ASM421653v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:42,938] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:42,938] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e49e14a-0236-42c5-bd27-390bf778a02d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:42,939] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e49e14a-0236-42c5-bd27-390bf778a02d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:42,963] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:57:42,964] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:57:42,964] [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
Isoptericola jiangsuensis	strain=DSM 21863	GCA_002563715.1	548579	548579	type	True	80.2341	614	1321	95	below_threshold
Isoptericola chiayiensis	strain=KCTC 19740	GCA_013149805.1	579446	579446	type	True	80.1655	570	1321	95	below_threshold
Isoptericola dokdonensis	strain=DS-3	GCA_001636295.1	372663	372663	type	True	80.1056	612	1321	95	below_threshold
Isoptericola sediminis	strain=JC619	GCA_013085345.1	2733572	2733572	type	True	79.9604	535	1321	95	below_threshold
Promicromonospora citrea	strain=ATCC 15908	GCA_013004695.1	43677	43677	type	True	79.7962	622	1321	95	below_threshold
Promicromonospora citrea	strain=JCM 3051	GCA_014647735.1	43677	43677	type	True	79.7422	655	1321	95	below_threshold
Promicromonospora sukumoe	strain=DSM 44121	GCA_014137995.1	88382	88382	type	True	79.6851	667	1321	95	below_threshold
Promicromonospora kroppenstedtii	strain=DSM 19349	GCA_000515355.1	440482	440482	type	True	79.658	583	1321	95	below_threshold
Cellulosimicrobium marinum	strain=NBRC 110994	GCA_020551945.1	1638992	1638992	type	True	79.5572	600	1321	95	below_threshold
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	79.5341	550	1321	95	below_threshold
Oerskovia douganii	strain=Sa1BUA8	GCA_015142735.1	2762210	2762210	type	True	79.4853	536	1321	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	79.4038	555	1321	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	79.2821	552	1321	95	below_threshold
Cellulosimicrobium arenosum	strain=KCTC 49039	GCA_014837295.1	2708133	2708133	type	True	79.2631	560	1321	95	below_threshold
Myceligenerans xiligouense	strain=DSM 15700	GCA_003814695.1	253184	253184	type	True	79.2422	541	1321	95	below_threshold
Cellulomonas soli	strain=DSM 24484	GCA_013409305.1	931535	931535	type	True	79.1816	497	1321	95	below_threshold
Cellulomonas fimi	strain=ATCC 484	GCA_000212695.1	1708	1708	type	True	79.1036	570	1321	95	below_threshold
Promicromonospora umidemergens	strain=DSM 22081	GCA_024171995.1	629679	629679	type	True	79.0866	575	1321	95	below_threshold
Cellulomonas fimi	strain=NCTC7547	GCA_900637695.1	1708	1708	type	True	79.061	573	1321	95	below_threshold
Cellulomonas flavigena	strain=DSM 20109	GCA_000092865.1	1711	1711	type	True	79.0044	539	1321	95	below_threshold
Myceligenerans salitolerans	strain=XHU 5031	GCA_017349295.1	1230528	1230528	type	True	78.9851	502	1321	95	below_threshold
Cellulomonas persica	strain=NBRC 101101	GCA_007989825.1	76861	76861	type	True	78.9734	525	1321	95	below_threshold
Cellulomonas biazotea	strain=NBRC12680	GCA_004306155.1	1709	1709	type	True	78.9087	523	1321	95	below_threshold
Cellulomonas uda	strain=NBRC 3747	GCA_006538705.1	1714	1714	type	True	78.9036	530	1321	95	below_threshold
Ruania albidiflava	strain=DSM 18029	GCA_000421225.1	366586	366586	type	True	77.042	277	1321	95	below_threshold
Flexivirga oryzae	strain=DSM 105369	GCA_014190805.1	1794944	1794944	type	True	76.9312	277	1321	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:42,966] [INFO] DFAST Taxonomy check result was written to GCF_004216535.1_ASM421653v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:42,967] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:42,967] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:42,967] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e49e14a-0236-42c5-bd27-390bf778a02d/dqc_reference/checkm_data
[2024-01-24 10:57:42,968] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:43,009] [INFO] Task started: CheckM
[2024-01-24 10:57:43,010] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004216535.1_ASM421653v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004216535.1_ASM421653v1_genomic.fna/checkm_input GCF_004216535.1_ASM421653v1_genomic.fna/checkm_result
[2024-01-24 10:58:52,708] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:52,710] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:52,734] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:52,734] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:52,734] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004216535.1_ASM421653v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:52,735] [INFO] Task started: Blastn
[2024-01-24 10:58:52,735] [INFO] Running command: blastn -query GCF_004216535.1_ASM421653v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e49e14a-0236-42c5-bd27-390bf778a02d/dqc_reference/reference_markers_gtdb.fasta -out GCF_004216535.1_ASM421653v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:54,947] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:54,952] [INFO] Selected 13 target genomes.
[2024-01-24 10:58:54,952] [INFO] Target genome list was writen to GCF_004216535.1_ASM421653v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:54,981] [INFO] Task started: fastANI
[2024-01-24 10:58:54,981] [INFO] Running command: fastANI --query /var/lib/cwl/stg9cd0d116-b0df-4900-9f55-bc7f2d726597/GCF_004216535.1_ASM421653v1_genomic.fna.gz --refList GCF_004216535.1_ASM421653v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004216535.1_ASM421653v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:07,587] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:07,604] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:07,604] [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_004216535.1	s__Xylanimonas ulmi	100.0	1320	1321	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Xylanimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004135345.1	s__Xylanimonas allomyrinae	84.9614	871	1321	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Xylanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135385.1	s__Xylanimonas sp004135385	83.851	789	1321	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Xylanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024965.1	s__Xylanimonas cellulosilytica	83.6697	798	1321	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	83.5598	742	1321	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Xylanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001592145.1	s__Xylanimonas pachnodae	82.2617	724	1321	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Xylanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003244315.1	s__Xylanimonas oleitrophica	82.0663	648	1321	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Xylanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000215105.1	s__Isoptericola variabilis_A	81.4444	658	1321	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	99.96	99.96	0.98	0.98	2	-
GCF_002563715.1	s__Isoptericola jiangsuensis	80.2265	613	1321	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	80.1458	572	1321	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Isoptericola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014837295.1	s__Cellulosimicrobium arenosum	79.3002	555	1321	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003851725.1	s__Cellulomonas algicola	79.1373	515	1321	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	97.47	95.68	0.95	0.94	3	-
GCF_004306155.1	s__Cellulomonas biazotea	78.9767	514	1321	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:07,606] [INFO] GTDB search result was written to GCF_004216535.1_ASM421653v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:07,606] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:07,611] [INFO] DFAST_QC result json was written to GCF_004216535.1_ASM421653v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:07,611] [INFO] DFAST_QC completed!
[2024-01-24 10:59:07,611] [INFO] Total running time: 0h2m2s