[2023-03-18 21:29:09,921] [INFO] DFAST_QC pipeline started.
[2023-03-18 21:29:09,921] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 21:29:09,921] [INFO] DQC Reference Directory: /var/lib/cwl/stg79dc3100-75ea-47d3-8c40-c557b250b78e/dqc_reference
[2023-03-18 21:29:11,011] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 21:29:11,011] [INFO] Task started: Prodigal
[2023-03-18 21:29:11,011] [INFO] Running command: cat /var/lib/cwl/stgfcbd1247-37df-44b3-a2d0-9d4d9dad4ee3/OceanDNA-b23043.fa | prodigal -d OceanDNA-b23043/cds.fna -a OceanDNA-b23043/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:29:38,813] [INFO] Task succeeded: Prodigal
[2023-03-18 21:29:38,813] [INFO] Task started: HMMsearch
[2023-03-18 21:29:38,813] [INFO] Running command: hmmsearch --tblout OceanDNA-b23043/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg79dc3100-75ea-47d3-8c40-c557b250b78e/dqc_reference/reference_markers.hmm OceanDNA-b23043/protein.faa > /dev/null
[2023-03-18 21:29:39,081] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:29:39,082] [INFO] Found 6/6 markers.
[2023-03-18 21:29:39,110] [INFO] Query marker FASTA was written to OceanDNA-b23043/markers.fasta
[2023-03-18 21:29:39,111] [INFO] Task started: Blastn
[2023-03-18 21:29:39,111] [INFO] Running command: blastn -query OceanDNA-b23043/markers.fasta -db /var/lib/cwl/stg79dc3100-75ea-47d3-8c40-c557b250b78e/dqc_reference/reference_markers.fasta -out OceanDNA-b23043/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:29:39,727] [INFO] Task succeeded: Blastn
[2023-03-18 21:29:39,729] [INFO] Selected 30 target genomes.
[2023-03-18 21:29:39,729] [INFO] Target genome list was writen to OceanDNA-b23043/target_genomes.txt
[2023-03-18 21:29:39,750] [INFO] Task started: fastANI
[2023-03-18 21:29:39,750] [INFO] Running command: fastANI --query /var/lib/cwl/stgfcbd1247-37df-44b3-a2d0-9d4d9dad4ee3/OceanDNA-b23043.fa --refList OceanDNA-b23043/target_genomes.txt --output OceanDNA-b23043/fastani_result.tsv --threads 1
[2023-03-18 21:29:59,928] [INFO] Task succeeded: fastANI
[2023-03-18 21:29:59,928] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg79dc3100-75ea-47d3-8c40-c557b250b78e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:29:59,928] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg79dc3100-75ea-47d3-8c40-c557b250b78e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:29:59,941] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:29:59,942] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 21:29:59,942] [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
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	75.1846	50	1072	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	75.1636	90	1072	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	75.1606	83	1072	95	below_threshold
Pseudoxanthomonas sangjuensis	strain=DSM 28345	GCA_010211755.1	1503750	1503750	type	True	75.1235	55	1072	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_002933415.1	215580	215580	type	True	75.0723	77	1072	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	75.0616	79	1072	95	below_threshold
Micromonospora chersina	strain=DSM 44151	GCA_900091475.1	47854	47854	type	True	74.8866	127	1072	95	below_threshold
Nannocystis exedens	strain=ATCC 25963	GCA_900112715.1	54	54	type	True	74.8839	266	1072	95	below_threshold
Nannocystis exedens	strain=DSM 71	GCA_002343915.1	54	54	type	True	74.8788	271	1072	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_003119195.2	1064539	1064539	type	True	74.8498	90	1072	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_008274945.1	192	192	type	True	74.8383	84	1072	95	below_threshold
Acuticoccus mangrovi	strain=B2012	GCA_016411865.1	2796142	2796142	type	True	74.8346	97	1072	95	below_threshold
Methylobacterium isbiliense	strain=DSM 17168	GCA_022179325.1	315478	315478	type	True	74.8309	134	1072	95	below_threshold
Longimicrobium terrae	strain=CB-286315	GCA_013000925.1	1639882	1639882	type	True	74.8202	65	1072	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_007827425.1	192	192	type	True	74.813	84	1072	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	74.7794	78	1072	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_002027385.1	192	192	type	True	74.7762	81	1072	95	below_threshold
Albimonas donghaensis	strain=DSM 17890	GCA_900106695.1	356660	356660	type	True	74.7722	90	1072	95	below_threshold
Oceanithermus profundus	strain=DSM 14977	GCA_000183745.1	187137	187137	type	True	74.7166	53	1072	95	below_threshold
Pseudoxanthomonas winnipegensis	strain=NML 130738	GCA_004283755.1	2480810	2480810	type	True	74.7136	57	1072	95	below_threshold
Agromyces flavus	strain=CPCC 202695	GCA_900104685.1	589382	589382	type	True	74.7123	88	1072	95	below_threshold
Agromyces flavus	strain=CCM 7623	GCA_014635805.1	589382	589382	type	True	74.7105	88	1072	95	below_threshold
Agromyces flavus	strain=CPCC 202695	GCA_004366335.2	589382	589382	type	True	74.7084	89	1072	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 21:29:59,942] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23043/tc_result.tsv
[2023-03-18 21:29:59,942] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:29:59,942] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:29:59,943] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg79dc3100-75ea-47d3-8c40-c557b250b78e/dqc_reference/checkm_data
[2023-03-18 21:29:59,943] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:30:00,043] [INFO] Task started: CheckM
[2023-03-18 21:30:00,043] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23043/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23043/checkm_input OceanDNA-b23043/checkm_result
[2023-03-18 21:31:06,503] [INFO] Task succeeded: CheckM
[2023-03-18 21:31:06,504] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.68%
Contamintation: 1.56%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-18 21:31:06,507] [INFO] ===== Completeness check finished =====
[2023-03-18 21:31:06,507] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:31:06,507] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23043/markers.fasta)
[2023-03-18 21:31:06,509] [INFO] Task started: Blastn
[2023-03-18 21:31:06,509] [INFO] Running command: blastn -query OceanDNA-b23043/markers.fasta -db /var/lib/cwl/stg79dc3100-75ea-47d3-8c40-c557b250b78e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23043/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:31:07,410] [INFO] Task succeeded: Blastn
[2023-03-18 21:31:07,411] [INFO] Selected 17 target genomes.
[2023-03-18 21:31:07,411] [INFO] Target genome list was writen to OceanDNA-b23043/target_genomes_gtdb.txt
[2023-03-18 21:31:07,428] [INFO] Task started: fastANI
[2023-03-18 21:31:07,428] [INFO] Running command: fastANI --query /var/lib/cwl/stgfcbd1247-37df-44b3-a2d0-9d4d9dad4ee3/OceanDNA-b23043.fa --refList OceanDNA-b23043/target_genomes_gtdb.txt --output OceanDNA-b23043/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:31:20,619] [INFO] Task succeeded: fastANI
[2023-03-18 21:31:20,629] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 21:31:20,629] [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_002862085.1	s__GCA-2862085 sp002862085	89.6271	916	1072	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2862085	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016779205.1	s__GCA-2862085 sp016779205	78.768	473	1072	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2862085	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007751475.1	s__GCA-2862085 sp007751475	78.2856	449	1072	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2862085	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480285.1	s__GCA-2862085 sp905480285	78.1154	396	1072	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2862085	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004357655.1	s__N075bin59 sp004357655	76.2983	186	1072	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__N075bin59	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903892045.1	s__F1-120-MAGs118 sp903892045	76.1997	186	1072	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__F1-120-MAGs118	95.0	99.41	99.41	0.87	0.87	3	-
GCA_002686265.1	s__GCA-2686265 sp002686265	76.1633	170	1072	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2686265	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903928115.1	s__F1-120-MAGs118 sp903928115	76.0924	170	1072	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__F1-120-MAGs118	95.0	99.83	99.80	0.95	0.95	3	-
GCA_016220035.1	s__JADJNY01 sp016220035	75.8486	201	1072	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JADJNY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125265.1	s__RI-242 sp016125265	75.8397	143	1072	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__RI-242	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003694875.1	s__J103 sp003694875	75.0753	60	1072	d__Bacteria;p__Planctomycetota;c__J058;o__J103;f__J103;g__J103	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390885.1	s__JAABRT01 sp011390885	75.0412	79	1072	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__JAABRT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795345.1	s__JAEUHO01 sp016795345	75.0304	175	1072	d__Bacteria;p__Planctomycetota;c__PLA2;o__PLA2;f__JAEUHO01;g__JAEUHO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013297655.1	s__JAAFHV01 sp013297655	74.8045	120	1072	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__JAAFHV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016201015.1	s__JACQDQ01 sp016201015	74.774	56	1072	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CACIAM-22H2;f__CACIAM-22H2;g__JACQDQ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 21:31:20,629] [INFO] GTDB search result was written to OceanDNA-b23043/result_gtdb.tsv
[2023-03-18 21:31:20,630] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:31:20,632] [INFO] DFAST_QC result json was written to OceanDNA-b23043/dqc_result.json
[2023-03-18 21:31:20,632] [INFO] DFAST_QC completed!
[2023-03-18 21:31:20,632] [INFO] Total running time: 0h2m11s