[2023-03-19 05:19:33,775] [INFO] DFAST_QC pipeline started.
[2023-03-19 05:19:33,776] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 05:19:33,776] [INFO] DQC Reference Directory: /var/lib/cwl/stg0e8cbfd0-b949-46a0-add0-ad2fb95bafa1/dqc_reference
[2023-03-19 05:19:35,400] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 05:19:35,401] [INFO] Task started: Prodigal
[2023-03-19 05:19:35,401] [INFO] Running command: cat /var/lib/cwl/stg43d7eab6-a2fe-4649-9c10-277a01568d0d/OceanDNA-b38223.fa | prodigal -d OceanDNA-b38223/cds.fna -a OceanDNA-b38223/protein.faa -g 11 -q > /dev/null
[2023-03-19 05:20:02,087] [INFO] Task succeeded: Prodigal
[2023-03-19 05:20:02,087] [INFO] Task started: HMMsearch
[2023-03-19 05:20:02,087] [INFO] Running command: hmmsearch --tblout OceanDNA-b38223/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0e8cbfd0-b949-46a0-add0-ad2fb95bafa1/dqc_reference/reference_markers.hmm OceanDNA-b38223/protein.faa > /dev/null
[2023-03-19 05:20:02,356] [INFO] Task succeeded: HMMsearch
[2023-03-19 05:20:02,357] [INFO] Found 6/6 markers.
[2023-03-19 05:20:02,380] [INFO] Query marker FASTA was written to OceanDNA-b38223/markers.fasta
[2023-03-19 05:20:02,381] [INFO] Task started: Blastn
[2023-03-19 05:20:02,381] [INFO] Running command: blastn -query OceanDNA-b38223/markers.fasta -db /var/lib/cwl/stg0e8cbfd0-b949-46a0-add0-ad2fb95bafa1/dqc_reference/reference_markers.fasta -out OceanDNA-b38223/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:20:03,199] [INFO] Task succeeded: Blastn
[2023-03-19 05:20:03,200] [INFO] Selected 24 target genomes.
[2023-03-19 05:20:03,200] [INFO] Target genome list was writen to OceanDNA-b38223/target_genomes.txt
[2023-03-19 05:20:03,215] [INFO] Task started: fastANI
[2023-03-19 05:20:03,215] [INFO] Running command: fastANI --query /var/lib/cwl/stg43d7eab6-a2fe-4649-9c10-277a01568d0d/OceanDNA-b38223.fa --refList OceanDNA-b38223/target_genomes.txt --output OceanDNA-b38223/fastani_result.tsv --threads 1
[2023-03-19 05:20:21,982] [INFO] Task succeeded: fastANI
[2023-03-19 05:20:21,982] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0e8cbfd0-b949-46a0-add0-ad2fb95bafa1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 05:20:21,982] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0e8cbfd0-b949-46a0-add0-ad2fb95bafa1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 05:20:21,996] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 05:20:21,996] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 05:20:21,996] [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	82.6412	975	1381	95	below_threshold
Halomonas smyrnensis	strain=AAD6	GCA_000265245.2	720605	720605	type	True	79.5665	508	1381	95	below_threshold
Halomonas halophila	strain=NBRC 102604	GCA_007989465.1	29573	29573	type	True	79.4958	506	1381	95	below_threshold
Halomonas stenophila	strain=CECT 7744	GCA_014192275.1	795312	795312	type	True	79.453	494	1381	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	79.384	514	1381	95	below_threshold
Halomonas organivorans	strain=CECT 5995	GCA_014192055.1	257772	257772	type	True	79.3288	536	1381	95	below_threshold
Halomonas ventosae	strain=CECT 5797	GCA_004363555.1	229007	229007	type	True	79.3103	489	1381	95	below_threshold
Halomonas aestuarii	strain=Hb3	GCA_001886615.1	1897729	1897729	type	True	79.298	461	1381	95	below_threshold
Halomonas campaniensis	strain=5AG	GCA_014193375.1	213554	213554	type	True	79.2629	484	1381	95	below_threshold
Halomonas borealis	strain=ATF 5.2	GCA_004798905.1	2508710	2508710	type	True	79.106	443	1381	95	below_threshold
Halomonas heilongjiangensis	strain=DSM 26881	GCA_002879645.1	1387883	1387883	type	True	79.0006	501	1381	95	below_threshold
Halomonas urmiana	strain=TBZ3	GCA_005780185.1	490901	490901	type	True	78.9721	478	1381	95	below_threshold
Halomonas heilongjiangensis	strain=9-2	GCA_003202165.1	1387883	1387883	type	True	78.9661	515	1381	95	below_threshold
Halomonas lactosivorans	strain=KCTC 52281	GCA_003254665.1	2185141	2185141	type	True	78.8455	466	1381	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	78.8049	393	1381	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	78.7168	377	1381	95	below_threshold
Halomonas cupida	strain=NBRC 102219	GCA_007991155.1	44933	44933	type	True	78.7166	519	1381	95	below_threshold
Halomonas cupida	strain=DSM 4740	GCA_900142755.1	44933	44933	type	True	78.7012	541	1381	95	below_threshold
Halomonas huangheensis	strain=BJGMM-B45	GCA_000470745.1	1178482	1178482	type	True	78.6619	488	1381	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	78.6506	472	1381	95	below_threshold
Halomonas huangheensis	strain=BJGMM-B45	GCA_001431725.1	1178482	1178482	type	True	78.6247	485	1381	95	below_threshold
Halomonas aerodenitrificans	strain=MCCC 1A11058	GCA_021404405.1	2733483	2733483	type	True	78.6188	440	1381	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	78.5605	423	1381	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	78.5267	435	1381	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 05:20:21,996] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38223/tc_result.tsv
[2023-03-19 05:20:21,996] [INFO] ===== Taxonomy check completed =====
[2023-03-19 05:20:21,997] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 05:20:21,997] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0e8cbfd0-b949-46a0-add0-ad2fb95bafa1/dqc_reference/checkm_data
[2023-03-19 05:20:21,998] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 05:20:22,004] [INFO] Task started: CheckM
[2023-03-19 05:20:22,004] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38223/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38223/checkm_input OceanDNA-b38223/checkm_result
[2023-03-19 05:21:27,073] [INFO] Task succeeded: CheckM
[2023-03-19 05:21:27,073] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 05:21:27,076] [INFO] ===== Completeness check finished =====
[2023-03-19 05:21:27,076] [INFO] ===== Start GTDB Search =====
[2023-03-19 05:21:27,076] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38223/markers.fasta)
[2023-03-19 05:21:27,077] [INFO] Task started: Blastn
[2023-03-19 05:21:27,077] [INFO] Running command: blastn -query OceanDNA-b38223/markers.fasta -db /var/lib/cwl/stg0e8cbfd0-b949-46a0-add0-ad2fb95bafa1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38223/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:21:28,461] [INFO] Task succeeded: Blastn
[2023-03-19 05:21:28,462] [INFO] Selected 18 target genomes.
[2023-03-19 05:21:28,462] [INFO] Target genome list was writen to OceanDNA-b38223/target_genomes_gtdb.txt
[2023-03-19 05:21:28,478] [INFO] Task started: fastANI
[2023-03-19 05:21:28,478] [INFO] Running command: fastANI --query /var/lib/cwl/stg43d7eab6-a2fe-4649-9c10-277a01568d0d/OceanDNA-b38223.fa --refList OceanDNA-b38223/target_genomes_gtdb.txt --output OceanDNA-b38223/fastani_result_gtdb.tsv --threads 1
[2023-03-19 05:21:44,108] [INFO] Task succeeded: fastANI
[2023-03-19 05:21:44,119] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 05:21:44,120] [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_017303055.1	s__Halomonas litopenaei_A	98.3121	1310	1381	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003045775.1	s__Halomonas litopenaei	82.6214	979	1381	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.31	97.80	0.93	0.89	11	-
GCA_002433675.1	s__Halomonas salina_B	82.0999	797	1381	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.49	99.49	0.75	0.75	2	-
GCF_000265245.1	s__Halomonas smyrnensis	79.5665	508	1381	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	79.5008	506	1381	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.43	97.59	0.92	0.89	4	-
GCF_014192275.1	s__Halomonas stenophila	79.4582	493	1381	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003056305.1	s__Halomonas denitrificans	79.3845	514	1381	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363555.1	s__Halomonas ventosae	79.3195	488	1381	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.59	95.59	0.89	0.89	2	-
GCF_014192055.1	s__Halomonas organivorans	79.3157	538	1381	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014193375.1	s__Halomonas campaniensis	79.2631	484	1381	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004798905.1	s__Halomonas borealis	79.0953	444	1381	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005780185.1	s__Halomonas urmiana	78.9722	478	1381	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003202205.1	s__Halomonas sp003202205	78.9265	506	1381	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104135.1	s__Halomonas shengliensis	78.8758	463	1381	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.66	95.66	0.79	0.79	2	-
GCF_001971685.1	s__Halomonas_B sp001971685	78.7718	423	1381	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142755.1	s__Halomonas cupida	78.7167	540	1381	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.98	99.98	1.00	1.00	2	-
GCF_001431725.1	s__Halomonas huangheensis	78.6334	484	1381	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_008329985.2	s__Halomonas sp008329985	78.4805	435	1381	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 05:21:44,120] [INFO] GTDB search result was written to OceanDNA-b38223/result_gtdb.tsv
[2023-03-19 05:21:44,120] [INFO] ===== GTDB Search completed =====
[2023-03-19 05:21:44,122] [INFO] DFAST_QC result json was written to OceanDNA-b38223/dqc_result.json
[2023-03-19 05:21:44,122] [INFO] DFAST_QC completed!
[2023-03-19 05:21:44,122] [INFO] Total running time: 0h2m10s