[2023-03-18 21:30:55,919] [INFO] DFAST_QC pipeline started.
[2023-03-18 21:30:55,919] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 21:30:55,920] [INFO] DQC Reference Directory: /var/lib/cwl/stg26927af8-0edc-4bfa-a070-7d910563d9a9/dqc_reference
[2023-03-18 21:30:57,077] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 21:30:57,078] [INFO] Task started: Prodigal
[2023-03-18 21:30:57,078] [INFO] Running command: cat /var/lib/cwl/stg0c418f22-5b36-4f39-9289-0bffe3b7b6e4/OceanDNA-b32721.fa | prodigal -d OceanDNA-b32721/cds.fna -a OceanDNA-b32721/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:31:06,529] [INFO] Task succeeded: Prodigal
[2023-03-18 21:31:06,529] [INFO] Task started: HMMsearch
[2023-03-18 21:31:06,529] [INFO] Running command: hmmsearch --tblout OceanDNA-b32721/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg26927af8-0edc-4bfa-a070-7d910563d9a9/dqc_reference/reference_markers.hmm OceanDNA-b32721/protein.faa > /dev/null
[2023-03-18 21:31:06,693] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:31:06,694] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg0c418f22-5b36-4f39-9289-0bffe3b7b6e4/OceanDNA-b32721.fa]
[2023-03-18 21:31:06,714] [INFO] Query marker FASTA was written to OceanDNA-b32721/markers.fasta
[2023-03-18 21:31:06,715] [INFO] Task started: Blastn
[2023-03-18 21:31:06,715] [INFO] Running command: blastn -query OceanDNA-b32721/markers.fasta -db /var/lib/cwl/stg26927af8-0edc-4bfa-a070-7d910563d9a9/dqc_reference/reference_markers.fasta -out OceanDNA-b32721/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:31:07,278] [INFO] Task succeeded: Blastn
[2023-03-18 21:31:07,279] [INFO] Selected 22 target genomes.
[2023-03-18 21:31:07,280] [INFO] Target genome list was writen to OceanDNA-b32721/target_genomes.txt
[2023-03-18 21:31:07,289] [INFO] Task started: fastANI
[2023-03-18 21:31:07,289] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c418f22-5b36-4f39-9289-0bffe3b7b6e4/OceanDNA-b32721.fa --refList OceanDNA-b32721/target_genomes.txt --output OceanDNA-b32721/fastani_result.tsv --threads 1
[2023-03-18 21:31:25,303] [INFO] Task succeeded: fastANI
[2023-03-18 21:31:25,303] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg26927af8-0edc-4bfa-a070-7d910563d9a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:31:25,303] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg26927af8-0edc-4bfa-a070-7d910563d9a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:31:25,311] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:31:25,311] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 21:31:25,312] [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
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	76.7813	101	415	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.5873	51	415	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	76.5317	105	415	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	76.5291	93	415	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	76.5089	94	415	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	76.4453	98	415	95	below_threshold
Azospirillum palustre	strain=B2	GCA_002573965.1	2044885	2044885	type	True	76.2217	74	415	95	below_threshold
Azospirillum halopraeferens	strain=DSM 3675	GCA_000429625.1	34010	34010	type	True	76.0107	76	415	95	below_threshold
Azospirillum picis	strain=IMMIB TAR-3	GCA_017876115.1	488438	488438	type	True	75.9876	87	415	95	below_threshold
Azospirillum melinis	strain=TMCY 0552	GCA_017876055.1	328839	328839	type	True	75.9677	79	415	95	below_threshold
Aminobacter ciceronei	strain=DSM 15910	GCA_014138625.1	150723	150723	type	True	75.9232	53	415	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	75.7582	61	415	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 21:31:25,312] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32721/tc_result.tsv
[2023-03-18 21:31:25,312] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:31:25,312] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:31:25,312] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg26927af8-0edc-4bfa-a070-7d910563d9a9/dqc_reference/checkm_data
[2023-03-18 21:31:25,313] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:31:25,317] [INFO] Task started: CheckM
[2023-03-18 21:31:25,317] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32721/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32721/checkm_input OceanDNA-b32721/checkm_result
[2023-03-18 21:31:53,492] [INFO] Task succeeded: CheckM
[2023-03-18 21:31:53,493] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 55.67%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 21:31:53,495] [INFO] ===== Completeness check finished =====
[2023-03-18 21:31:53,495] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:31:53,495] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32721/markers.fasta)
[2023-03-18 21:31:53,496] [INFO] Task started: Blastn
[2023-03-18 21:31:53,496] [INFO] Running command: blastn -query OceanDNA-b32721/markers.fasta -db /var/lib/cwl/stg26927af8-0edc-4bfa-a070-7d910563d9a9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32721/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:31:54,224] [INFO] Task succeeded: Blastn
[2023-03-18 21:31:54,225] [INFO] Selected 20 target genomes.
[2023-03-18 21:31:54,225] [INFO] Target genome list was writen to OceanDNA-b32721/target_genomes_gtdb.txt
[2023-03-18 21:31:54,250] [INFO] Task started: fastANI
[2023-03-18 21:31:54,250] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c418f22-5b36-4f39-9289-0bffe3b7b6e4/OceanDNA-b32721.fa --refList OceanDNA-b32721/target_genomes_gtdb.txt --output OceanDNA-b32721/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:32:07,676] [INFO] Task succeeded: fastANI
[2023-03-18 21:32:07,686] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 21:32:07,686] [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_009691025.1	s__SHWB01 sp009691025	78.1494	89	415	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__SHWB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018702955.1	s__UBA8079 sp018702955	77.3906	107	415	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	77.3365	119	415	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	99.89	99.79	0.96	0.96	6	-
GCA_011087645.1	s__JABDJY01 sp011087645	77.294	133	415	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	77.1745	107	415	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__JABDJY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017643325.1	s__JABJAG01 sp017643325	77.1204	110	415	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__JABJAG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002727315.1	s__UBA8079 sp002727315	76.9604	81	415	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003116015.1	s__Azospirillum sp003116015	76.4878	99	415	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869645.1	s__SHVW01 sp016869645	76.4249	89	415	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVW01;f__SHVW01;g__SHVW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869415.1	s__VGEI01 sp016869415	76.3774	56	415	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CACIAM-22H2;f__CACIAM-22H2;g__VGEI01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000496075.1	s__Lutibaculum baratangense	76.3304	54	415	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Tepidamorphaceae;g__Lutibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523655.1	s__Bin65 sp011523655	76.3275	72	415	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Bin65;f__Bin65;g__Bin65	95.0	95.25	95.16	0.87	0.83	5	-
GCA_009377375.1	s__WHUE01 sp009377375	76.304	101	415	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA2964;g__WHUE01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177515.1	s__Azospirillum oryzae_A	76.0919	73	415	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016583645.1	s__Rhodovibrio sodomensis	76.0222	62	415	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Rhodovibrionaceae;g__Rhodovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876115.1	s__Azospirillum picis	75.9715	88	415	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793165.1	s__CAIOSQ01 sp016793165	75.789	86	415	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CACIAM-22H2;f__CACIAM-22H2;g__CAIOSQ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 21:32:07,686] [INFO] GTDB search result was written to OceanDNA-b32721/result_gtdb.tsv
[2023-03-18 21:32:07,686] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:32:07,688] [INFO] DFAST_QC result json was written to OceanDNA-b32721/dqc_result.json
[2023-03-18 21:32:07,688] [INFO] DFAST_QC completed!
[2023-03-18 21:32:07,688] [INFO] Total running time: 0h1m12s