[2023-03-15 08:09:45,411] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:09:45,412] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:09:45,412] [INFO] DQC Reference Directory: /var/lib/cwl/stg4d26a11d-d5b5-43fb-b564-d3b1f28630f2/dqc_reference
[2023-03-15 08:09:46,693] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:09:46,694] [INFO] Task started: Prodigal
[2023-03-15 08:09:46,694] [INFO] Running command: cat /var/lib/cwl/stg1beb2707-0f47-4204-b614-36358c275992/OceanDNA-b2773.fa | prodigal -d OceanDNA-b2773/cds.fna -a OceanDNA-b2773/protein.faa -g 11 -q > /dev/null
[2023-03-15 08:09:58,333] [INFO] Task succeeded: Prodigal
[2023-03-15 08:09:58,333] [INFO] Task started: HMMsearch
[2023-03-15 08:09:58,333] [INFO] Running command: hmmsearch --tblout OceanDNA-b2773/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4d26a11d-d5b5-43fb-b564-d3b1f28630f2/dqc_reference/reference_markers.hmm OceanDNA-b2773/protein.faa > /dev/null
[2023-03-15 08:09:58,565] [INFO] Task succeeded: HMMsearch
[2023-03-15 08:09:58,565] [INFO] Found 6/6 markers.
[2023-03-15 08:09:58,580] [INFO] Query marker FASTA was written to OceanDNA-b2773/markers.fasta
[2023-03-15 08:09:58,581] [INFO] Task started: Blastn
[2023-03-15 08:09:58,581] [INFO] Running command: blastn -query OceanDNA-b2773/markers.fasta -db /var/lib/cwl/stg4d26a11d-d5b5-43fb-b564-d3b1f28630f2/dqc_reference/reference_markers.fasta -out OceanDNA-b2773/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:09:59,737] [INFO] Task succeeded: Blastn
[2023-03-15 08:09:59,737] [INFO] Selected 23 target genomes.
[2023-03-15 08:09:59,738] [INFO] Target genome list was writen to OceanDNA-b2773/target_genomes.txt
[2023-03-15 08:09:59,770] [INFO] Task started: fastANI
[2023-03-15 08:09:59,770] [INFO] Running command: fastANI --query /var/lib/cwl/stg1beb2707-0f47-4204-b614-36358c275992/OceanDNA-b2773.fa --refList OceanDNA-b2773/target_genomes.txt --output OceanDNA-b2773/fastani_result.tsv --threads 1
[2023-03-15 08:10:12,792] [INFO] Task succeeded: fastANI
[2023-03-15 08:10:12,793] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4d26a11d-d5b5-43fb-b564-d3b1f28630f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 08:10:12,793] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4d26a11d-d5b5-43fb-b564-d3b1f28630f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 08:10:12,806] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 08:10:12,806] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 08:10:12,806] [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
Conyzicola nivalis	strain=CGMCC 1.12813	GCA_014639655.1	1477021	1477021	type	True	80.647	342	621	95	below_threshold
Conyzicola lurida	strain=DSM 105784	GCA_014204935.1	1172621	1172621	type	True	80.5274	382	621	95	below_threshold
Protaetiibacter intestinalis	strain=2DFWR-13	GCA_003627075.1	2419774	2419774	type	True	80.1126	333	621	95	below_threshold
Protaetiibacter larvae	strain=KACC 19322	GCA_008365275.1	2592654	2592654	type	True	79.874	298	621	95	below_threshold
Galbitalea soli	strain=DSM 105515	GCA_013410525.1	1268042	1268042	type	True	79.8117	300	621	95	below_threshold
Galbitalea soli	strain=NBRC 108727	GCA_010686725.1	1268042	1268042	type	True	79.7548	299	621	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_021922985.1	31965	28447	type	True	79.6267	272	621	95	below_threshold
Clavibacter phaseoli	strain=LPPA 982	GCA_021922925.1	1734031	1734031	type	True	79.5872	285	621	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	79.5608	277	621	95	below_threshold
Clavibacter michiganensis	strain=LMG7333	GCA_021216655.1	28447	28447	suspected-type	True	79.5202	264	621	95	below_threshold
Clavibacter zhangzhiyongii	strain=DM1	GCA_014775655.1	2768071	2768071	type	True	79.509	275	621	95	below_threshold
Rathayibacter festucae	strain=DSM 15932	GCA_004011135.1	110937	110937	type	True	79.3826	323	621	95	below_threshold
Leifsonia aquatica	strain=ATCC 14665	GCA_000469485.1	144185	144185	type	True	79.3498	250	621	95	below_threshold
Cryobacterium tepidiphilum	strain=NEAU-85	GCA_003716325.1	2486026	2486026	type	True	79.3098	234	621	95	below_threshold
Lacisediminihabitans profunda	strain=CHu50b-6-2	GCA_008040105.1	2594790	2594790	type	True	79.282	307	621	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=CFBP 2404	GCA_003693415.1	33014	28447	type	True	79.201	277	621	95	below_threshold
Leifsonia aquatica	strain=DSM 20146	GCA_014190775.1	144185	144185	type	True	79.1544	302	621	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=ATCC 10253	GCA_003076355.1	33014	28447	type	True	79.1175	282	621	95	below_threshold
Lacisediminihabitans changchengi	strain=G11-30	GCA_016634425.1	2787634	2787634	type	True	78.9602	274	621	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	78.7356	291	621	95	below_threshold
Microbacterium hydrocarbonoxydans	strain=DSM 16089	GCA_900105205.1	273678	273678	suspected-type	True	78.2628	222	621	95	below_threshold
Microbacterium hydrocarbonoxydans	strain=NBRC 103074	GCA_001552455.1	273678	273678	suspected-type	True	78.2541	221	621	95	below_threshold
Glaciihabitans tibetensis	strain=CGMCC 1.12484	GCA_003003265.1	1266600	1266600	type	True	78.252	219	621	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 08:10:12,807] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2773/tc_result.tsv
[2023-03-15 08:10:12,807] [INFO] ===== Taxonomy check completed =====
[2023-03-15 08:10:12,807] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 08:10:12,807] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4d26a11d-d5b5-43fb-b564-d3b1f28630f2/dqc_reference/checkm_data
[2023-03-15 08:10:12,808] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 08:10:12,816] [INFO] Task started: CheckM
[2023-03-15 08:10:12,816] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2773/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2773/checkm_input OceanDNA-b2773/checkm_result
[2023-03-15 08:10:44,567] [INFO] Task succeeded: CheckM
[2023-03-15 08:10:44,567] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 08:10:44,570] [INFO] ===== Completeness check finished =====
[2023-03-15 08:10:44,570] [INFO] ===== Start GTDB Search =====
[2023-03-15 08:10:44,570] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2773/markers.fasta)
[2023-03-15 08:10:44,571] [INFO] Task started: Blastn
[2023-03-15 08:10:44,571] [INFO] Running command: blastn -query OceanDNA-b2773/markers.fasta -db /var/lib/cwl/stg4d26a11d-d5b5-43fb-b564-d3b1f28630f2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2773/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:10:46,377] [INFO] Task succeeded: Blastn
[2023-03-15 08:10:46,379] [INFO] Selected 16 target genomes.
[2023-03-15 08:10:46,380] [INFO] Target genome list was writen to OceanDNA-b2773/target_genomes_gtdb.txt
[2023-03-15 08:10:46,392] [INFO] Task started: fastANI
[2023-03-15 08:10:46,392] [INFO] Running command: fastANI --query /var/lib/cwl/stg1beb2707-0f47-4204-b614-36358c275992/OceanDNA-b2773.fa --refList OceanDNA-b2773/target_genomes_gtdb.txt --output OceanDNA-b2773/fastani_result_gtdb.tsv --threads 1
[2023-03-15 08:10:56,004] [INFO] Task succeeded: fastANI
[2023-03-15 08:10:56,014] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 08:10:56,014] [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
GCA_013297645.1	s__JAAFHU01 sp013297645	84.8753	407	621	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__JAAFHU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001725325.1	s__Rhodoglobus sp001725325	80.8988	382	621	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus	95.0	100.00	100.00	1.00	1.00	3	-
GCF_014639655.1	s__Conyzicola nivalis	80.6294	343	621	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Conyzicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004310685.1	s__Conyzicola arctica	80.5864	356	621	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Conyzicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204935.1	s__Conyzicola lurida	80.5268	382	621	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Conyzicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903920435.1	s__Rhodoglobus sp903920435	80.3363	346	621	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoglobus	95.0	98.49	97.73	0.85	0.78	4	-
GCF_013408685.1	s__Schumannella luteola	80.1873	333	621	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Schumannella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006517435.1	s__Schumannella sp006517435	80.1192	321	621	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Schumannella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797715.1	s__Diaminobutyricimonas aerilata	79.9323	314	621	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Diaminobutyricimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898835.1	s__Protaetiibacter sp001898835	79.7614	340	621	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003243275.1	s__Protaetiibacter sp003243275	79.6485	329	621	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017833035.1	s__Frigoribacterium sp017833035	79.638	271	621	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frigoribacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001429165.1	s__Agromyces sp001429165	79.3942	295	621	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002151125.1	s__Clavibacter michiganensis_C	79.3425	277	621	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Clavibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008040105.1	s__Lacisediminihabitans profunda	79.2817	307	621	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Lacisediminihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016634425.1	s__Lacisediminihabitans sp016634425	78.9602	274	621	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Lacisediminihabitans	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 08:10:56,014] [INFO] GTDB search result was written to OceanDNA-b2773/result_gtdb.tsv
[2023-03-15 08:10:56,014] [INFO] ===== GTDB Search completed =====
[2023-03-15 08:10:56,017] [INFO] DFAST_QC result json was written to OceanDNA-b2773/dqc_result.json
[2023-03-15 08:10:56,017] [INFO] DFAST_QC completed!
[2023-03-15 08:10:56,017] [INFO] Total running time: 0h1m11s