[2023-03-18 08:17:17,732] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:17:17,732] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:17:17,732] [INFO] DQC Reference Directory: /var/lib/cwl/stg9bcf9479-663a-4388-a8a1-75929f4837cb/dqc_reference
[2023-03-18 08:17:18,942] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:17:18,943] [INFO] Task started: Prodigal
[2023-03-18 08:17:18,943] [INFO] Running command: cat /var/lib/cwl/stg38c5a3a5-eade-456e-a2f0-ca336463e910/OceanDNA-b36585.fa | prodigal -d OceanDNA-b36585/cds.fna -a OceanDNA-b36585/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:17:42,082] [INFO] Task succeeded: Prodigal
[2023-03-18 08:17:42,083] [INFO] Task started: HMMsearch
[2023-03-18 08:17:42,083] [INFO] Running command: hmmsearch --tblout OceanDNA-b36585/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9bcf9479-663a-4388-a8a1-75929f4837cb/dqc_reference/reference_markers.hmm OceanDNA-b36585/protein.faa > /dev/null
[2023-03-18 08:17:42,325] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:17:42,325] [INFO] Found 6/6 markers.
[2023-03-18 08:17:42,348] [INFO] Query marker FASTA was written to OceanDNA-b36585/markers.fasta
[2023-03-18 08:17:42,348] [INFO] Task started: Blastn
[2023-03-18 08:17:42,348] [INFO] Running command: blastn -query OceanDNA-b36585/markers.fasta -db /var/lib/cwl/stg9bcf9479-663a-4388-a8a1-75929f4837cb/dqc_reference/reference_markers.fasta -out OceanDNA-b36585/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:17:43,121] [INFO] Task succeeded: Blastn
[2023-03-18 08:17:43,122] [INFO] Selected 14 target genomes.
[2023-03-18 08:17:43,122] [INFO] Target genome list was writen to OceanDNA-b36585/target_genomes.txt
[2023-03-18 08:17:43,130] [INFO] Task started: fastANI
[2023-03-18 08:17:43,130] [INFO] Running command: fastANI --query /var/lib/cwl/stg38c5a3a5-eade-456e-a2f0-ca336463e910/OceanDNA-b36585.fa --refList OceanDNA-b36585/target_genomes.txt --output OceanDNA-b36585/fastani_result.tsv --threads 1
[2023-03-18 08:17:54,245] [INFO] Task succeeded: fastANI
[2023-03-18 08:17:54,246] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9bcf9479-663a-4388-a8a1-75929f4837cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:17:54,246] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9bcf9479-663a-4388-a8a1-75929f4837cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:17:54,254] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:17:54,255] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 08:17:54,255] [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
Alcanivorax borkumensis	strain=SK2	GCA_000009365.1	59754	59754	type	True	82.6624	754	1176	95	below_threshold
Alcanivorax jadensis	strain=T9	GCA_000756655.1	64988	64988	type	True	81.3069	764	1176	95	below_threshold
Alcanivorax hongdengensis	strain=A-11-3	GCA_000300995.1	519051	519051	type	True	80.4458	652	1176	95	below_threshold
Alcanivorax profundi	strain=MTEO17	GCA_003597125.1	2338368	2338368	type	True	80.2607	669	1176	95	below_threshold
Alcanivorax nanhaiticus	strain=19-m-6	GCA_000756665.1	1177154	1177154	type	True	80.1474	633	1176	95	below_threshold
Alcanivorax sediminis	strain=PA15-N-34	GCA_009601165.1	2663008	2663008	type	True	79.8829	620	1176	95	below_threshold
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	78.3725	384	1176	95	below_threshold
Alcanivorax gelatiniphagus	strain=MEBiC 08158	GCA_005938655.1	1194167	1194167	type	True	78.3689	423	1176	95	below_threshold
Alcanivorax balearicus	strain=MACL04	GCA_025532145.1	413232	413232	type	True	78.1011	329	1176	95	below_threshold
Alcanivorax limicola	strain=JB21	GCA_019931215.1	2874102	2874102	type	True	77.1863	234	1176	95	below_threshold
Marinobacter arenosus	strain=CAU 1620	GCA_019264345.1	2856822	2856822	type	True	76.2462	91	1176	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=DSM 6698	GCA_003851905.1	587851	587753	type	True	76.0379	98	1176	95	below_threshold
Pseudomonas chlororaphis subsp. aureofaciens	strain=NBRC 3521	GCA_000813225.1	587851	587753	type	True	76.0368	98	1176	95	below_threshold
Oceanobacter mangrovi	strain=SM2-42	GCA_019740315.1	2862510	2862510	type	True	75.9939	56	1176	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 08:17:54,255] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36585/tc_result.tsv
[2023-03-18 08:17:54,255] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:17:54,255] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:17:54,255] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9bcf9479-663a-4388-a8a1-75929f4837cb/dqc_reference/checkm_data
[2023-03-18 08:17:54,256] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:17:54,261] [INFO] Task started: CheckM
[2023-03-18 08:17:54,261] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36585/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36585/checkm_input OceanDNA-b36585/checkm_result
[2023-03-18 08:18:52,443] [INFO] Task succeeded: CheckM
[2023-03-18 08:18:52,444] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:18:52,446] [INFO] ===== Completeness check finished =====
[2023-03-18 08:18:52,447] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:18:52,447] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36585/markers.fasta)
[2023-03-18 08:18:52,447] [INFO] Task started: Blastn
[2023-03-18 08:18:52,447] [INFO] Running command: blastn -query OceanDNA-b36585/markers.fasta -db /var/lib/cwl/stg9bcf9479-663a-4388-a8a1-75929f4837cb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36585/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:18:53,718] [INFO] Task succeeded: Blastn
[2023-03-18 08:18:53,719] [INFO] Selected 10 target genomes.
[2023-03-18 08:18:53,719] [INFO] Target genome list was writen to OceanDNA-b36585/target_genomes_gtdb.txt
[2023-03-18 08:18:53,729] [INFO] Task started: fastANI
[2023-03-18 08:18:53,729] [INFO] Running command: fastANI --query /var/lib/cwl/stg38c5a3a5-eade-456e-a2f0-ca336463e910/OceanDNA-b36585.fa --refList OceanDNA-b36585/target_genomes_gtdb.txt --output OceanDNA-b36585/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:19:02,340] [INFO] Task succeeded: fastANI
[2023-03-18 08:19:02,346] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 08:19:02,346] [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_002726155.1	s__Alcanivorax sp002726155	99.9716	1146	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000155615.1	s__Alcanivorax sp000155615	92.9687	1090	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	97.88	97.69	0.92	0.89	4	-
GCA_002733835.1	s__Alcanivorax sp002733835	90.727	977	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000009365.1	s__Alcanivorax borkumensis	82.6515	755	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	99.54	99.30	0.96	0.95	6	-
GCA_003862375.1	s__Alcanivorax jadensis_A	81.5941	735	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	99.67	99.67	0.92	0.92	2	-
GCF_000756655.1	s__Alcanivorax jadensis	81.315	762	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.11	97.73	0.92	0.86	7	-
GCF_900107995.1	s__Alcanivorax sp900107995	81.2194	753	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.42	98.03	0.93	0.89	9	-
GCF_000300995.1	s__Alcanivorax hongdengensis	80.4372	654	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017794965.1	s__Alcanivorax sp017794965	80.349	667	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000756665.1	s__Alcanivorax nanhaiticus	80.1576	631	1176	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 08:19:02,347] [INFO] GTDB search result was written to OceanDNA-b36585/result_gtdb.tsv
[2023-03-18 08:19:02,347] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:19:02,348] [INFO] DFAST_QC result json was written to OceanDNA-b36585/dqc_result.json
[2023-03-18 08:19:02,348] [INFO] DFAST_QC completed!
[2023-03-18 08:19:02,348] [INFO] Total running time: 0h1m45s