[2023-06-30 05:50:39,923] [INFO] DFAST_QC pipeline started.
[2023-06-30 05:50:39,926] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 05:50:39,926] [INFO] DQC Reference Directory: /var/lib/cwl/stgb74561df-7fd0-47fd-b0a3-a293a8978dd5/dqc_reference
[2023-06-30 05:50:41,698] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 05:50:41,700] [INFO] Task started: Prodigal
[2023-06-30 05:50:41,700] [INFO] Running command: gunzip -c /var/lib/cwl/stg8c8c5cab-354a-49d2-aa97-c22de6e47437/GCA_903841975.1_freshwater_MAG_---_LaPlata-1m-b_bin-128_genomic.fna.gz | prodigal -d GCA_903841975.1_freshwater_MAG_---_LaPlata-1m-b_bin-128_genomic.fna/cds.fna -a GCA_903841975.1_freshwater_MAG_---_LaPlata-1m-b_bin-128_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 05:50:45,901] [INFO] Task succeeded: Prodigal
[2023-06-30 05:50:45,901] [INFO] Task started: HMMsearch
[2023-06-30 05:50:45,902] [INFO] Running command: hmmsearch --tblout GCA_903841975.1_freshwater_MAG_---_LaPlata-1m-b_bin-128_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb74561df-7fd0-47fd-b0a3-a293a8978dd5/dqc_reference/reference_markers.hmm GCA_903841975.1_freshwater_MAG_---_LaPlata-1m-b_bin-128_genomic.fna/protein.faa > /dev/null
[2023-06-30 05:50:46,142] [INFO] Task succeeded: HMMsearch
[2023-06-30 05:50:46,144] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8c8c5cab-354a-49d2-aa97-c22de6e47437/GCA_903841975.1_freshwater_MAG_---_LaPlata-1m-b_bin-128_genomic.fna.gz]
[2023-06-30 05:50:46,169] [INFO] Query marker FASTA was written to GCA_903841975.1_freshwater_MAG_---_LaPlata-1m-b_bin-128_genomic.fna/markers.fasta
[2023-06-30 05:50:46,170] [INFO] Task started: Blastn
[2023-06-30 05:50:46,170] [INFO] Running command: blastn -query GCA_903841975.1_freshwater_MAG_---_LaPlata-1m-b_bin-128_genomic.fna/markers.fasta -db /var/lib/cwl/stgb74561df-7fd0-47fd-b0a3-a293a8978dd5/dqc_reference/reference_markers.fasta -out GCA_903841975.1_freshwater_MAG_---_LaPlata-1m-b_bin-128_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 05:50:47,079] [INFO] Task succeeded: Blastn
[2023-06-30 05:50:47,085] [INFO] Selected 31 target genomes.
[2023-06-30 05:50:47,085] [INFO] Target genome list was writen to GCA_903841975.1_freshwater_MAG_---_LaPlata-1m-b_bin-128_genomic.fna/target_genomes.txt
[2023-06-30 05:50:47,092] [INFO] Task started: fastANI
[2023-06-30 05:50:47,092] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c8c5cab-354a-49d2-aa97-c22de6e47437/GCA_903841975.1_freshwater_MAG_---_LaPlata-1m-b_bin-128_genomic.fna.gz --refList GCA_903841975.1_freshwater_MAG_---_LaPlata-1m-b_bin-128_genomic.fna/target_genomes.txt --output GCA_903841975.1_freshwater_MAG_---_LaPlata-1m-b_bin-128_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 05:51:09,908] [INFO] Task succeeded: fastANI
[2023-06-30 05:51:09,909] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb74561df-7fd0-47fd-b0a3-a293a8978dd5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 05:51:09,909] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb74561df-7fd0-47fd-b0a3-a293a8978dd5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 05:51:09,936] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 05:51:09,936] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 05:51:09,937] [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
Gaiella occulta	strain=F2-233	GCA_003351045.1	1002870	1002870	type	True	76.4675	152	449	95	below_threshold
Conexibacter arvalis	strain=DSM 23288	GCA_014199525.1	912552	912552	type	True	76.0807	217	449	95	below_threshold
Miltoncostaea marina	strain=SCSIO 60955	GCA_018141525.1	2843215	2843215	type	True	76.0635	180	449	95	below_threshold
Capillimicrobium parvum	strain=0166_1	GCA_021172045.1	2884022	2884022	type	True	75.798	223	449	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	75.7972	184	449	95	below_threshold
Miltoncostaea oceani	strain=SCSIO 61214	GCA_018141545.1	2843216	2843216	type	True	75.7967	165	449	95	below_threshold
Baekduia soli	strain=BR7-21	GCA_007970665.1	496014	496014	type	True	75.7764	195	449	95	below_threshold
Conexibacter woesei	strain=DSM 14684	GCA_000025265.1	191495	191495	type	True	75.6974	212	449	95	below_threshold
Ottowia beijingensis	strain=GCS-AN-3	GCA_013423955.1	1207057	1207057	type	True	75.597	51	449	95	below_threshold
Patulibacter minatonensis	strain=DSM 18081	GCA_000519325.1	298163	298163	type	True	75.4819	193	449	95	below_threshold
Nocardioides plantarum	strain=DSM 11054	GCA_006346395.1	29299	29299	type	True	75.313	125	449	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	75.2831	67	449	95	below_threshold
Luteimonas colneyensis	strain=Sa2BVA3	GCA_014836665.1	2762230	2762230	type	True	75.2221	77	449	95	below_threshold
Demequina pelophila	strain=NBRC 109393	GCA_000971175.1	1638984	1638984	type	True	75.191	87	449	95	below_threshold
Actinacidiphila epipremni	strain=PRB2-1	GCA_012034175.1	2053013	2053013	type	True	75.1644	161	449	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	75.1635	136	449	95	below_threshold
Arenimonas metalli	strain=CF5-1	GCA_000747155.1	948077	948077	type	True	75.1615	77	449	95	below_threshold
Nocardioides litoris	strain=DSM 103718	GCA_006346315.1	1926648	1926648	type	True	75.1327	153	449	95	below_threshold
Stenotrophomonas daejeonensis	strain=JCM 16244	GCA_001431505.1	659018	659018	type	True	75.1209	68	449	95	below_threshold
Ramlibacter monticola	strain=KACC 19175	GCA_016722785.1	1926872	1926872	type	True	75.0851	95	449	95	below_threshold
Streptomyces phaeofaciens	strain=JCM 4125	GCA_014648915.1	68254	68254	type	True	75.0578	161	449	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	75.0266	138	449	95	below_threshold
Microbacterium oryzae	strain=MB-10	GCA_009735645.1	743009	743009	type	True	75.019	85	449	95	below_threshold
Micromonospora jinlongensis	strain=DSM 45876	GCA_013410645.1	1287877	1287877	type	True	75.0057	85	449	95	below_threshold
Stenotrophomonas acidaminiphila	strain=DSM 13117	GCA_024221815.1	128780	128780	type	True	75.0021	52	449	95	below_threshold
Amycolatopsis anabasis	strain=EGI 650086	GCA_009765355.1	1840409	1840409	type	True	74.9706	124	449	95	below_threshold
Microbacterium halophytorum	strain=YJYP 303	GCA_002970975.1	2067568	2067568	type	True	74.9694	94	449	95	below_threshold
Lysobacter defluvii	strain=IMMIB APB-9	GCA_000769985.1	391738	391738	type	True	74.9659	54	449	95	below_threshold
Micromonospora polyrhachis	strain=DSM 45886	GCA_014203835.1	1282883	1282883	type	True	74.8917	53	449	95	below_threshold
Lysobacter defluvii	strain=DSM 18482	GCA_000423325.1	391738	391738	type	True	74.8714	68	449	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 05:51:09,939] [INFO] DFAST Taxonomy check result was written to GCA_903841975.1_freshwater_MAG_---_LaPlata-1m-b_bin-128_genomic.fna/tc_result.tsv
[2023-06-30 05:51:09,940] [INFO] ===== Taxonomy check completed =====
[2023-06-30 05:51:09,940] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 05:51:09,940] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb74561df-7fd0-47fd-b0a3-a293a8978dd5/dqc_reference/checkm_data
[2023-06-30 05:51:09,942] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 05:51:09,966] [INFO] Task started: CheckM
[2023-06-30 05:51:09,966] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903841975.1_freshwater_MAG_---_LaPlata-1m-b_bin-128_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903841975.1_freshwater_MAG_---_LaPlata-1m-b_bin-128_genomic.fna/checkm_input GCA_903841975.1_freshwater_MAG_---_LaPlata-1m-b_bin-128_genomic.fna/checkm_result
[2023-06-30 05:51:29,020] [INFO] Task succeeded: CheckM
[2023-06-30 05:51:29,021] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.41%
Contamintation: 5.09%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-06-30 05:51:29,044] [INFO] ===== Completeness check finished =====
[2023-06-30 05:51:29,044] [INFO] ===== Start GTDB Search =====
[2023-06-30 05:51:29,045] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903841975.1_freshwater_MAG_---_LaPlata-1m-b_bin-128_genomic.fna/markers.fasta)
[2023-06-30 05:51:29,045] [INFO] Task started: Blastn
[2023-06-30 05:51:29,045] [INFO] Running command: blastn -query GCA_903841975.1_freshwater_MAG_---_LaPlata-1m-b_bin-128_genomic.fna/markers.fasta -db /var/lib/cwl/stgb74561df-7fd0-47fd-b0a3-a293a8978dd5/dqc_reference/reference_markers_gtdb.fasta -out GCA_903841975.1_freshwater_MAG_---_LaPlata-1m-b_bin-128_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 05:51:30,636] [INFO] Task succeeded: Blastn
[2023-06-30 05:51:30,641] [INFO] Selected 7 target genomes.
[2023-06-30 05:51:30,641] [INFO] Target genome list was writen to GCA_903841975.1_freshwater_MAG_---_LaPlata-1m-b_bin-128_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 05:51:30,646] [INFO] Task started: fastANI
[2023-06-30 05:51:30,646] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c8c5cab-354a-49d2-aa97-c22de6e47437/GCA_903841975.1_freshwater_MAG_---_LaPlata-1m-b_bin-128_genomic.fna.gz --refList GCA_903841975.1_freshwater_MAG_---_LaPlata-1m-b_bin-128_genomic.fna/target_genomes_gtdb.txt --output GCA_903841975.1_freshwater_MAG_---_LaPlata-1m-b_bin-128_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 05:51:33,691] [INFO] Task succeeded: fastANI
[2023-06-30 05:51:33,703] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 05:51:33,703] [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_903873565.1	s__F1-60-MAGs149 sp903873565	98.7677	377	449	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__F1-60-MAGs149;g__F1-60-MAGs149	95.0	98.96	98.77	0.82	0.80	5	conclusive
GCA_016870485.1	s__F1-60-MAGs149 sp016870485	91.114	404	449	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__F1-60-MAGs149;g__F1-60-MAGs149	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903847495.1	s__F1-60-MAGs149 sp903847495	82.102	253	449	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__F1-60-MAGs149;g__F1-60-MAGs149	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903960645.1	s__F1-60-MAGs149 sp903960645	81.9439	283	449	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__F1-60-MAGs149;g__F1-60-MAGs149	95.0	98.37	98.10	0.78	0.76	11	-
GCA_016462095.1	s__F1-60-MAGs149 sp016462095	78.9654	206	449	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__F1-60-MAGs149;g__F1-60-MAGs149	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005798855.1	s__F1-60-MAGs149 sp005798855	78.4223	187	449	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__F1-60-MAGs149;g__F1-60-MAGs149	95.0	99.87	99.85	0.93	0.91	3	-
GCA_009694475.1	s__F1-60-MAGs149 sp009694475	78.3688	198	449	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__F1-60-MAGs149;g__F1-60-MAGs149	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 05:51:33,705] [INFO] GTDB search result was written to GCA_903841975.1_freshwater_MAG_---_LaPlata-1m-b_bin-128_genomic.fna/result_gtdb.tsv
[2023-06-30 05:51:33,706] [INFO] ===== GTDB Search completed =====
[2023-06-30 05:51:33,710] [INFO] DFAST_QC result json was written to GCA_903841975.1_freshwater_MAG_---_LaPlata-1m-b_bin-128_genomic.fna/dqc_result.json
[2023-06-30 05:51:33,710] [INFO] DFAST_QC completed!
[2023-06-30 05:51:33,710] [INFO] Total running time: 0h0m54s