[2023-03-17 23:08:31,938] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:08:31,939] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:08:31,939] [INFO] DQC Reference Directory: /var/lib/cwl/stga15e40fc-ff14-4a64-a056-60e46180567c/dqc_reference
[2023-03-17 23:08:33,154] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:08:33,155] [INFO] Task started: Prodigal
[2023-03-17 23:08:33,155] [INFO] Running command: cat /var/lib/cwl/stg07908683-613b-4827-9849-6bdc7103cf85/OceanDNA-b2814.fa | prodigal -d OceanDNA-b2814/cds.fna -a OceanDNA-b2814/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:08:38,682] [INFO] Task succeeded: Prodigal
[2023-03-17 23:08:38,682] [INFO] Task started: HMMsearch
[2023-03-17 23:08:38,682] [INFO] Running command: hmmsearch --tblout OceanDNA-b2814/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga15e40fc-ff14-4a64-a056-60e46180567c/dqc_reference/reference_markers.hmm OceanDNA-b2814/protein.faa > /dev/null
[2023-03-17 23:08:38,821] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:08:38,821] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg07908683-613b-4827-9849-6bdc7103cf85/OceanDNA-b2814.fa]
[2023-03-17 23:08:38,839] [INFO] Query marker FASTA was written to OceanDNA-b2814/markers.fasta
[2023-03-17 23:08:38,840] [INFO] Task started: Blastn
[2023-03-17 23:08:38,840] [INFO] Running command: blastn -query OceanDNA-b2814/markers.fasta -db /var/lib/cwl/stga15e40fc-ff14-4a64-a056-60e46180567c/dqc_reference/reference_markers.fasta -out OceanDNA-b2814/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:08:39,589] [INFO] Task succeeded: Blastn
[2023-03-17 23:08:39,593] [INFO] Selected 15 target genomes.
[2023-03-17 23:08:39,594] [INFO] Target genome list was writen to OceanDNA-b2814/target_genomes.txt
[2023-03-17 23:08:39,602] [INFO] Task started: fastANI
[2023-03-17 23:08:39,602] [INFO] Running command: fastANI --query /var/lib/cwl/stg07908683-613b-4827-9849-6bdc7103cf85/OceanDNA-b2814.fa --refList OceanDNA-b2814/target_genomes.txt --output OceanDNA-b2814/fastani_result.tsv --threads 1
[2023-03-17 23:08:47,360] [INFO] Task succeeded: fastANI
[2023-03-17 23:08:47,361] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga15e40fc-ff14-4a64-a056-60e46180567c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:08:47,361] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga15e40fc-ff14-4a64-a056-60e46180567c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:08:47,370] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:08:47,370] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 23:08:47,370] [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
Chryseoglobus frigidaquae	strain=DSM 23889	GCA_009664385.2	424758	424758	type	True	83.0171	201	249	95	below_threshold
Chryseoglobus frigidaquae	strain=DSM 23889	GCA_014200395.1	424758	424758	type	True	82.9981	202	249	95	below_threshold
Microcella putealis	strain=CV2	GCA_004216575.1	337005	337005	type	True	80.1981	168	249	95	below_threshold
Microcella putealis	strain=DSM 19627	GCA_006716545.1	337005	337005	type	True	80.0741	168	249	95	below_threshold
Protaetiibacter larvae	strain=KACC 19322	GCA_008365275.1	2592654	2592654	type	True	78.9891	119	249	95	below_threshold
Protaetiibacter intestinalis	strain=2DFWR-13	GCA_003627075.1	2419774	2419774	type	True	78.7251	139	249	95	below_threshold
Herbiconiux flava	strain=DSM 26474	GCA_013409865.1	881268	881268	type	True	78.383	116	249	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	78.1788	122	249	95	below_threshold
Agromyces subbeticus	strain=DSM 16689	GCA_000421565.1	293890	293890	type	True	78.1567	127	249	95	below_threshold
Herbiconiux moechotypicola	strain=KCTC 19653	GCA_024979255.1	637393	637393	type	True	78.1392	117	249	95	below_threshold
Agromyces flavus	strain=CPCC 202695	GCA_004366335.2	589382	589382	type	True	77.9516	126	249	95	below_threshold
Agromyces marinus	strain=DSM 26151	GCA_021442325.1	1389020	1389020	type	True	77.9373	116	249	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	77.9368	140	249	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	77.8708	127	249	95	below_threshold
Microbacterium commune	strain=Re1	GCA_014836945.1	2762219	2762219	type	True	77.6738	88	249	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 23:08:47,372] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2814/tc_result.tsv
[2023-03-17 23:08:47,373] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:08:47,373] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:08:47,374] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga15e40fc-ff14-4a64-a056-60e46180567c/dqc_reference/checkm_data
[2023-03-17 23:08:47,374] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:08:47,525] [INFO] Task started: CheckM
[2023-03-17 23:08:47,525] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2814/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2814/checkm_input OceanDNA-b2814/checkm_result
[2023-03-17 23:09:07,208] [INFO] Task succeeded: CheckM
[2023-03-17 23:09:07,208] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.19%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 23:09:07,218] [INFO] ===== Completeness check finished =====
[2023-03-17 23:09:07,218] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:09:07,218] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2814/markers.fasta)
[2023-03-17 23:09:07,219] [INFO] Task started: Blastn
[2023-03-17 23:09:07,219] [INFO] Running command: blastn -query OceanDNA-b2814/markers.fasta -db /var/lib/cwl/stga15e40fc-ff14-4a64-a056-60e46180567c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2814/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:09:08,492] [INFO] Task succeeded: Blastn
[2023-03-17 23:09:08,496] [INFO] Selected 12 target genomes.
[2023-03-17 23:09:08,496] [INFO] Target genome list was writen to OceanDNA-b2814/target_genomes_gtdb.txt
[2023-03-17 23:09:08,506] [INFO] Task started: fastANI
[2023-03-17 23:09:08,506] [INFO] Running command: fastANI --query /var/lib/cwl/stg07908683-613b-4827-9849-6bdc7103cf85/OceanDNA-b2814.fa --refList OceanDNA-b2814/target_genomes_gtdb.txt --output OceanDNA-b2814/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:09:13,357] [INFO] Task succeeded: fastANI
[2023-03-17 23:09:13,365] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 23:09:13,365] [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_005778835.1	s__Chryseoglobus sp005778835	89.691	214	249	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Chryseoglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002423075.1	s__Chryseoglobus sp002423075	88.1251	171	249	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Chryseoglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002280615.1	s__Chryseoglobus sp002280615	85.0932	139	249	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Chryseoglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464255.1	s__Chryseoglobus sp001464255	84.6715	183	249	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Chryseoglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200395.1	s__Chryseoglobus frigidaquae	82.9981	202	249	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Chryseoglobus	95.0	100.00	100.00	1.00	1.00	2	-
GCA_013297625.1	s__Chryseoglobus sp013297625	82.208	192	249	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Chryseoglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013414345.1	s__Marinisubtilis indicus	81.8164	195	249	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Marinisubtilis	95.0	96.33	95.90	0.85	0.83	6	-
GCF_014595885.1	s__Yonghaparkia alkaliphila_A	81.7093	194	249	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009371975.2	s__Marinisubtilis pacificus	81.6474	211	249	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Marinisubtilis	95.0	97.81	97.81	0.83	0.83	2	-
GCA_012530535.1	s__Yonghaparkia sp012530535	81.3969	188	249	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005502445.1	s__Yonghaparkia sp005502445	81.0867	174	249	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005777405.1	s__Chryseoglobus sp005777405	80.6052	176	249	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Chryseoglobus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 23:09:13,366] [INFO] GTDB search result was written to OceanDNA-b2814/result_gtdb.tsv
[2023-03-17 23:09:13,368] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:09:13,370] [INFO] DFAST_QC result json was written to OceanDNA-b2814/dqc_result.json
[2023-03-17 23:09:13,370] [INFO] DFAST_QC completed!
[2023-03-17 23:09:13,370] [INFO] Total running time: 0h0m41s