[2023-03-15 14:06:11,261] [INFO] DFAST_QC pipeline started.
[2023-03-15 14:06:11,261] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 14:06:11,261] [INFO] DQC Reference Directory: /var/lib/cwl/stg6fd40262-5ced-4228-8d95-66b58374226c/dqc_reference
[2023-03-15 14:06:12,360] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 14:06:12,360] [INFO] Task started: Prodigal
[2023-03-15 14:06:12,360] [INFO] Running command: cat /var/lib/cwl/stg4f5f1b7f-ecb8-445a-b8b2-d99563e0e80d/OceanDNA-b32706.fa | prodigal -d OceanDNA-b32706/cds.fna -a OceanDNA-b32706/protein.faa -g 11 -q > /dev/null
[2023-03-15 14:06:30,710] [INFO] Task succeeded: Prodigal
[2023-03-15 14:06:30,710] [INFO] Task started: HMMsearch
[2023-03-15 14:06:30,710] [INFO] Running command: hmmsearch --tblout OceanDNA-b32706/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6fd40262-5ced-4228-8d95-66b58374226c/dqc_reference/reference_markers.hmm OceanDNA-b32706/protein.faa > /dev/null
[2023-03-15 14:06:30,913] [INFO] Task succeeded: HMMsearch
[2023-03-15 14:06:30,914] [INFO] Found 6/6 markers.
[2023-03-15 14:06:30,934] [INFO] Query marker FASTA was written to OceanDNA-b32706/markers.fasta
[2023-03-15 14:06:30,935] [INFO] Task started: Blastn
[2023-03-15 14:06:30,935] [INFO] Running command: blastn -query OceanDNA-b32706/markers.fasta -db /var/lib/cwl/stg6fd40262-5ced-4228-8d95-66b58374226c/dqc_reference/reference_markers.fasta -out OceanDNA-b32706/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:06:31,645] [INFO] Task succeeded: Blastn
[2023-03-15 14:06:31,646] [INFO] Selected 33 target genomes.
[2023-03-15 14:06:31,647] [INFO] Target genome list was writen to OceanDNA-b32706/target_genomes.txt
[2023-03-15 14:06:31,667] [INFO] Task started: fastANI
[2023-03-15 14:06:31,667] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f5f1b7f-ecb8-445a-b8b2-d99563e0e80d/OceanDNA-b32706.fa --refList OceanDNA-b32706/target_genomes.txt --output OceanDNA-b32706/fastani_result.tsv --threads 1
[2023-03-15 14:06:53,213] [INFO] Task succeeded: fastANI
[2023-03-15 14:06:53,213] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6fd40262-5ced-4228-8d95-66b58374226c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 14:06:53,214] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6fd40262-5ced-4228-8d95-66b58374226c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 14:06:53,222] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 14:06:53,222] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 14:06:53,222] [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
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	76.0614	60	963	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.0457	63	963	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	75.8561	81	963	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	75.8326	62	963	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	75.6685	59	963	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_007827425.1	192	192	type	True	75.6396	64	963	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_008274945.1	192	192	type	True	75.5652	64	963	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_002027385.1	192	192	type	True	75.5434	63	963	95	below_threshold
Magnetospirillum magnetotacticum	strain=MS-1	GCA_000829825.1	188	188	type	True	75.4945	60	963	95	below_threshold
Bosea robiniae	strain=DSM 26672	GCA_900102525.1	1036780	1036780	type	True	75.352	52	963	95	below_threshold
Azospirillum ramasamyi	strain=M2T2B2	GCA_003233655.1	682998	682998	type	True	75.337	56	963	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 14:06:53,222] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32706/tc_result.tsv
[2023-03-15 14:06:53,224] [INFO] ===== Taxonomy check completed =====
[2023-03-15 14:06:53,224] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 14:06:53,224] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6fd40262-5ced-4228-8d95-66b58374226c/dqc_reference/checkm_data
[2023-03-15 14:06:53,225] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 14:06:53,230] [INFO] Task started: CheckM
[2023-03-15 14:06:53,230] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32706/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32706/checkm_input OceanDNA-b32706/checkm_result
[2023-03-15 14:07:41,275] [INFO] Task succeeded: CheckM
[2023-03-15 14:07:41,276] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 14:07:41,281] [INFO] ===== Completeness check finished =====
[2023-03-15 14:07:41,282] [INFO] ===== Start GTDB Search =====
[2023-03-15 14:07:41,282] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32706/markers.fasta)
[2023-03-15 14:07:41,283] [INFO] Task started: Blastn
[2023-03-15 14:07:41,283] [INFO] Running command: blastn -query OceanDNA-b32706/markers.fasta -db /var/lib/cwl/stg6fd40262-5ced-4228-8d95-66b58374226c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32706/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:07:42,566] [INFO] Task succeeded: Blastn
[2023-03-15 14:07:42,569] [INFO] Selected 22 target genomes.
[2023-03-15 14:07:42,569] [INFO] Target genome list was writen to OceanDNA-b32706/target_genomes_gtdb.txt
[2023-03-15 14:07:42,595] [INFO] Task started: fastANI
[2023-03-15 14:07:42,595] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f5f1b7f-ecb8-445a-b8b2-d99563e0e80d/OceanDNA-b32706.fa --refList OceanDNA-b32706/target_genomes_gtdb.txt --output OceanDNA-b32706/fastani_result_gtdb.tsv --threads 1
[2023-03-15 14:07:56,107] [INFO] Task succeeded: fastANI
[2023-03-15 14:07:56,114] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 14:07:56,115] [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_018666195.1	s__JABJAG01 sp018666195	83.3336	659	963	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__JABJAG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018702955.1	s__UBA8079 sp018702955	77.9063	351	963	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	99.54	99.39	0.93	0.91	5	-
GCA_018667335.1	s__UBA8079 sp018667335	77.7788	397	963	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	99.89	99.79	0.96	0.96	6	-
GCA_002727315.1	s__UBA8079 sp002727315	77.5364	285	963	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017643325.1	s__JABJAG01 sp017643325	77.2498	304	963	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__JABJAG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002724635.1	s__UBA8079 sp002724635	76.8831	221	963	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011087645.1	s__JABDJY01 sp011087645	76.184	176	963	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__JABDJY01	95.0	99.97	99.97	0.97	0.97	2	-
GCA_013003285.1	s__JABDJY01 sp013003285	76.1796	150	963	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__JABDJY01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904705.1	s__Nisaea sp014904705	76.0614	60	963	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001618175.1	s__Oceanibaculum pacificum	75.8748	80	963	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002281855.1	s__Reyranella sp002281855	75.6706	52	963	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	99.99	99.99	0.99	0.99	3	-
--------------------------------------------------------------------------------
[2023-03-15 14:07:56,117] [INFO] GTDB search result was written to OceanDNA-b32706/result_gtdb.tsv
[2023-03-15 14:07:56,118] [INFO] ===== GTDB Search completed =====
[2023-03-15 14:07:56,120] [INFO] DFAST_QC result json was written to OceanDNA-b32706/dqc_result.json
[2023-03-15 14:07:56,120] [INFO] DFAST_QC completed!
[2023-03-15 14:07:56,120] [INFO] Total running time: 0h1m45s