[2023-03-17 11:08:00,267] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:08:00,268] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:08:00,268] [INFO] DQC Reference Directory: /var/lib/cwl/stge1e05ff0-7ef1-4eab-9bfa-06314e97245d/dqc_reference
[2023-03-17 11:08:01,418] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:08:01,419] [INFO] Task started: Prodigal
[2023-03-17 11:08:01,419] [INFO] Running command: cat /var/lib/cwl/stg14547998-2122-4be1-bd62-c0791c1d2127/OceanDNA-b38305.fa | prodigal -d OceanDNA-b38305/cds.fna -a OceanDNA-b38305/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:08:25,474] [INFO] Task succeeded: Prodigal
[2023-03-17 11:08:25,475] [INFO] Task started: HMMsearch
[2023-03-17 11:08:25,475] [INFO] Running command: hmmsearch --tblout OceanDNA-b38305/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge1e05ff0-7ef1-4eab-9bfa-06314e97245d/dqc_reference/reference_markers.hmm OceanDNA-b38305/protein.faa > /dev/null
[2023-03-17 11:08:25,700] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:08:25,700] [INFO] Found 6/6 markers.
[2023-03-17 11:08:25,739] [INFO] Query marker FASTA was written to OceanDNA-b38305/markers.fasta
[2023-03-17 11:08:25,740] [INFO] Task started: Blastn
[2023-03-17 11:08:25,740] [INFO] Running command: blastn -query OceanDNA-b38305/markers.fasta -db /var/lib/cwl/stge1e05ff0-7ef1-4eab-9bfa-06314e97245d/dqc_reference/reference_markers.fasta -out OceanDNA-b38305/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:08:26,602] [INFO] Task succeeded: Blastn
[2023-03-17 11:08:26,605] [INFO] Selected 24 target genomes.
[2023-03-17 11:08:26,605] [INFO] Target genome list was writen to OceanDNA-b38305/target_genomes.txt
[2023-03-17 11:08:26,621] [INFO] Task started: fastANI
[2023-03-17 11:08:26,621] [INFO] Running command: fastANI --query /var/lib/cwl/stg14547998-2122-4be1-bd62-c0791c1d2127/OceanDNA-b38305.fa --refList OceanDNA-b38305/target_genomes.txt --output OceanDNA-b38305/fastani_result.tsv --threads 1
[2023-03-17 11:08:45,956] [INFO] Task succeeded: fastANI
[2023-03-17 11:08:45,956] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge1e05ff0-7ef1-4eab-9bfa-06314e97245d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:08:45,957] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge1e05ff0-7ef1-4eab-9bfa-06314e97245d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:08:45,971] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2023-03-17 11:08:45,971] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-17 11:08:45,971] [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 litopenaei	strain=SYSU ZJ2214	GCA_003045775.1	2109328	2109328	type	True	95.0734	1184	1279	95	conclusive
Halomonas smyrnensis	strain=AAD6	GCA_000265245.2	720605	720605	type	True	81.7355	581	1279	95	below_threshold
Halomonas halophila	strain=NBRC 102604	GCA_007989465.1	29573	29573	type	True	81.6092	585	1279	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	81.5875	607	1279	95	below_threshold
Halomonas stenophila	strain=CECT 7744	GCA_014192275.1	795312	795312	type	True	81.2658	605	1279	95	below_threshold
Halomonas organivorans	strain=CECT 5995	GCA_014192055.1	257772	257772	type	True	81.1303	625	1279	95	below_threshold
Halomonas saccharevitans	strain=CGMCC 1.6493	GCA_900116405.1	416872	416872	type	True	81.0546	553	1279	95	below_threshold
Halomonas nitroreducens	strain=11S	GCA_003966155.1	447425	447425	type	True	81.0288	619	1279	95	below_threshold
Halomonas ventosae	strain=CECT 5797	GCA_004363555.1	229007	229007	type	True	81.0279	592	1279	95	below_threshold
Halomonas campaniensis	strain=5AG	GCA_014193375.1	213554	213554	type	True	80.9552	569	1279	95	below_threshold
Halomonas urmiana	strain=TBZ3	GCA_005780185.1	490901	490901	type	True	80.9544	578	1279	95	below_threshold
Halomonas heilongjiangensis	strain=9-2	GCA_003202165.1	1387883	1387883	type	True	80.8751	584	1279	95	below_threshold
Halomonas borealis	strain=ATF 5.2	GCA_004798905.1	2508710	2508710	type	True	80.8712	550	1279	95	below_threshold
Halomonas heilongjiangensis	strain=DSM 26881	GCA_002879645.1	1387883	1387883	type	True	80.8064	584	1279	95	below_threshold
Halomonas alimentaria	strain=DSM 15356	GCA_009902005.1	147248	147248	type	True	80.7738	504	1279	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	80.6489	530	1279	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	80.5229	549	1279	95	below_threshold
Halomonas lactosivorans	strain=KCTC 52281	GCA_003254665.1	2185141	2185141	type	True	80.4793	556	1279	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	80.1105	502	1279	95	below_threshold
Halomonas aerodenitrificans	strain=MCCC 1A11058	GCA_021404405.1	2733483	2733483	type	True	80.0219	518	1279	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	79.9399	496	1279	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	79.7792	458	1279	95	below_threshold
Halomonas cupida	strain=NBRC 102219	GCA_007991155.1	44933	44933	type	True	79.4089	537	1279	95	below_threshold
Halomonas cupida	strain=DSM 4740	GCA_900142755.1	44933	44933	type	True	79.3757	570	1279	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 11:08:45,973] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38305/tc_result.tsv
[2023-03-17 11:08:45,976] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:08:45,976] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:08:45,976] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge1e05ff0-7ef1-4eab-9bfa-06314e97245d/dqc_reference/checkm_data
[2023-03-17 11:08:45,977] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:08:45,985] [INFO] Task started: CheckM
[2023-03-17 11:08:45,985] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38305/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38305/checkm_input OceanDNA-b38305/checkm_result
[2023-03-17 11:09:46,278] [INFO] Task succeeded: CheckM
[2023-03-17 11:09:46,279] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.09%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 11:09:46,331] [INFO] ===== Completeness check finished =====
[2023-03-17 11:09:46,331] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:09:46,331] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38305/markers.fasta)
[2023-03-17 11:09:46,332] [INFO] Task started: Blastn
[2023-03-17 11:09:46,332] [INFO] Running command: blastn -query OceanDNA-b38305/markers.fasta -db /var/lib/cwl/stge1e05ff0-7ef1-4eab-9bfa-06314e97245d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38305/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:09:47,949] [INFO] Task succeeded: Blastn
[2023-03-17 11:09:47,957] [INFO] Selected 13 target genomes.
[2023-03-17 11:09:47,957] [INFO] Target genome list was writen to OceanDNA-b38305/target_genomes_gtdb.txt
[2023-03-17 11:09:48,150] [INFO] Task started: fastANI
[2023-03-17 11:09:48,150] [INFO] Running command: fastANI --query /var/lib/cwl/stg14547998-2122-4be1-bd62-c0791c1d2127/OceanDNA-b38305.fa --refList OceanDNA-b38305/target_genomes_gtdb.txt --output OceanDNA-b38305/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:09:58,505] [INFO] Task succeeded: fastANI
[2023-03-17 11:09:58,513] [INFO] Found 13 fastANI hits (2 hits with ANI > circumscription radius)
[2023-03-17 11:09:58,513] [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_002433675.1	s__Halomonas salina_B	99.403	1027	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.49	99.49	0.75	0.75	2	inconclusive
GCF_003045775.1	s__Halomonas litopenaei	95.0734	1184	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.31	97.80	0.93	0.89	11	inconclusive
GCF_017303055.1	s__Halomonas litopenaei_A	82.5852	889	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000265245.1	s__Halomonas smyrnensis	81.7233	582	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.45	98.45	0.89	0.89	2	-
GCF_007989465.1	s__Halomonas halophila	81.6093	585	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.43	97.59	0.92	0.89	4	-
GCF_003056305.1	s__Halomonas denitrificans	81.5692	608	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363755.1	s__Halomonas sp009363755	81.4354	603	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014192275.1	s__Halomonas stenophila	81.2813	603	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116405.1	s__Halomonas saccharevitans	81.055	553	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002549795.1	s__Halomonas beimenensis	81.0068	604	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401555.1	s__Halomonas sp018401555	80.6038	475	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003552795.1	s__Halomonas sp003552795	80.4385	389	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010977575.1	s__Halomonas_B socia	80.1036	522	1279	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 11:09:58,514] [INFO] GTDB search result was written to OceanDNA-b38305/result_gtdb.tsv
[2023-03-17 11:09:58,515] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:09:58,520] [INFO] DFAST_QC result json was written to OceanDNA-b38305/dqc_result.json
[2023-03-17 11:09:58,520] [INFO] DFAST_QC completed!
[2023-03-17 11:09:58,520] [INFO] Total running time: 0h1m58s