[2023-03-18 08:36:16,001] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:36:16,001] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:36:16,001] [INFO] DQC Reference Directory: /var/lib/cwl/stg3afd287c-a9b6-4d1a-882c-63685a3008f2/dqc_reference
[2023-03-18 08:36:17,826] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:36:17,826] [INFO] Task started: Prodigal
[2023-03-18 08:36:17,826] [INFO] Running command: cat /var/lib/cwl/stgb65b4f0b-fe36-4a73-b4c5-4ff2c5816716/OceanDNA-b38353.fa | prodigal -d OceanDNA-b38353/cds.fna -a OceanDNA-b38353/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:36:40,705] [INFO] Task succeeded: Prodigal
[2023-03-18 08:36:40,706] [INFO] Task started: HMMsearch
[2023-03-18 08:36:40,706] [INFO] Running command: hmmsearch --tblout OceanDNA-b38353/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3afd287c-a9b6-4d1a-882c-63685a3008f2/dqc_reference/reference_markers.hmm OceanDNA-b38353/protein.faa > /dev/null
[2023-03-18 08:36:40,938] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:36:40,938] [INFO] Found 6/6 markers.
[2023-03-18 08:36:40,964] [INFO] Query marker FASTA was written to OceanDNA-b38353/markers.fasta
[2023-03-18 08:36:40,965] [INFO] Task started: Blastn
[2023-03-18 08:36:40,965] [INFO] Running command: blastn -query OceanDNA-b38353/markers.fasta -db /var/lib/cwl/stg3afd287c-a9b6-4d1a-882c-63685a3008f2/dqc_reference/reference_markers.fasta -out OceanDNA-b38353/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:36:41,843] [INFO] Task succeeded: Blastn
[2023-03-18 08:36:41,844] [INFO] Selected 19 target genomes.
[2023-03-18 08:36:41,844] [INFO] Target genome list was writen to OceanDNA-b38353/target_genomes.txt
[2023-03-18 08:36:41,900] [INFO] Task started: fastANI
[2023-03-18 08:36:41,900] [INFO] Running command: fastANI --query /var/lib/cwl/stgb65b4f0b-fe36-4a73-b4c5-4ff2c5816716/OceanDNA-b38353.fa --refList OceanDNA-b38353/target_genomes.txt --output OceanDNA-b38353/fastani_result.tsv --threads 1
[2023-03-18 08:36:57,321] [INFO] Task succeeded: fastANI
[2023-03-18 08:36:57,321] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3afd287c-a9b6-4d1a-882c-63685a3008f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:36:57,321] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3afd287c-a9b6-4d1a-882c-63685a3008f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:36:57,333] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:36:57,333] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 08:36:57,333] [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
Halomonas taeanensis	strain=BH539	GCA_900100755.1	284577	284577	type	True	91.1123	1013	1231	95	below_threshold
Halomonas niordiana	strain=ATF 5.4	GCA_004798965.1	2508711	2508711	type	True	84.5892	885	1231	95	below_threshold
Halomonas smyrnensis	strain=AAD6	GCA_000265245.2	720605	720605	type	True	81.1123	635	1231	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	81.0637	622	1231	95	below_threshold
Halomonas halophila	strain=NBRC 102604	GCA_007989465.1	29573	29573	type	True	81.0544	628	1231	95	below_threshold
Halomonas ventosae	strain=CECT 5797	GCA_004363555.1	229007	229007	type	True	80.8781	617	1231	95	below_threshold
Halomonas salipaludis	strain=WRN001	GCA_002286975.1	2032625	2032625	type	True	80.6079	603	1231	95	below_threshold
Halomonas nitroreducens	strain=11S	GCA_003966155.1	447425	447425	type	True	80.5687	641	1231	95	below_threshold
Halomonas campaniensis	strain=5AG	GCA_014193375.1	213554	213554	type	True	80.4945	574	1231	95	below_threshold
Halomonas pacifica	strain=NBRC 102220	GCA_007989625.1	77098	77098	type	True	80.4609	573	1231	95	below_threshold
Halomonas heilongjiangensis	strain=DSM 26881	GCA_002879645.1	1387883	1387883	type	True	80.3782	589	1231	95	below_threshold
Halomonas heilongjiangensis	strain=9-2	GCA_003202165.1	1387883	1387883	type	True	80.3702	611	1231	95	below_threshold
Halomonas pantelleriensis	strain=AAP	GCA_900102875.1	48727	48727	type	True	80.2931	576	1231	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	80.2214	544	1231	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	80.0251	552	1231	95	below_threshold
Halomonas aerodenitrificans	strain=MCCC 1A11058	GCA_021404405.1	2733483	2733483	type	True	79.8419	528	1231	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	79.7612	523	1231	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	79.6007	541	1231	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	79.5075	511	1231	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 08:36:57,334] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38353/tc_result.tsv
[2023-03-18 08:36:57,334] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:36:57,334] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:36:57,334] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3afd287c-a9b6-4d1a-882c-63685a3008f2/dqc_reference/checkm_data
[2023-03-18 08:36:57,335] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:36:57,341] [INFO] Task started: CheckM
[2023-03-18 08:36:57,341] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38353/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38353/checkm_input OceanDNA-b38353/checkm_result
[2023-03-18 08:37:54,014] [INFO] Task succeeded: CheckM
[2023-03-18 08:37:54,014] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:37:54,026] [INFO] ===== Completeness check finished =====
[2023-03-18 08:37:54,026] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:37:54,026] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38353/markers.fasta)
[2023-03-18 08:37:54,027] [INFO] Task started: Blastn
[2023-03-18 08:37:54,027] [INFO] Running command: blastn -query OceanDNA-b38353/markers.fasta -db /var/lib/cwl/stg3afd287c-a9b6-4d1a-882c-63685a3008f2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38353/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:37:55,635] [INFO] Task succeeded: Blastn
[2023-03-18 08:37:55,637] [INFO] Selected 6 target genomes.
[2023-03-18 08:37:55,637] [INFO] Target genome list was writen to OceanDNA-b38353/target_genomes_gtdb.txt
[2023-03-18 08:37:55,640] [INFO] Task started: fastANI
[2023-03-18 08:37:55,640] [INFO] Running command: fastANI --query /var/lib/cwl/stgb65b4f0b-fe36-4a73-b4c5-4ff2c5816716/OceanDNA-b38353.fa --refList OceanDNA-b38353/target_genomes_gtdb.txt --output OceanDNA-b38353/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:38:01,169] [INFO] Task succeeded: fastANI
[2023-03-18 08:38:01,173] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 08:38:01,173] [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_013349955.1	s__Halomonas_E taeanensis_B	98.5443	1104	1231	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_E	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003268885.1	s__Halomonas_E taeanensis_A	91.2874	1032	1231	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100755.1	s__Halomonas_E taeanensis	91.1123	1013	1231	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_E	95.0	98.15	98.15	0.92	0.92	2	-
GCF_014840935.1	s__Halomonas_E sp014840935	85.6892	884	1231	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004798965.1	s__Halomonas_E niordiana	84.5692	887	1231	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012062845.1	s__Halomonas_E sp012062845	84.0767	789	1231	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 08:38:01,175] [INFO] GTDB search result was written to OceanDNA-b38353/result_gtdb.tsv
[2023-03-18 08:38:01,175] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:38:01,178] [INFO] DFAST_QC result json was written to OceanDNA-b38353/dqc_result.json
[2023-03-18 08:38:01,178] [INFO] DFAST_QC completed!
[2023-03-18 08:38:01,178] [INFO] Total running time: 0h1m45s