[2023-03-18 00:53:42,863] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:53:42,863] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:53:42,863] [INFO] DQC Reference Directory: /var/lib/cwl/stgb40f1eb3-5017-4355-9322-dc550af35e2f/dqc_reference
[2023-03-18 00:53:44,415] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:53:44,415] [INFO] Task started: Prodigal
[2023-03-18 00:53:44,415] [INFO] Running command: cat /var/lib/cwl/stg8258b615-4e3e-4868-99d7-dfe6bcf9c39d/OceanDNA-b36597.fa | prodigal -d OceanDNA-b36597/cds.fna -a OceanDNA-b36597/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:54:05,898] [INFO] Task succeeded: Prodigal
[2023-03-18 00:54:05,899] [INFO] Task started: HMMsearch
[2023-03-18 00:54:05,899] [INFO] Running command: hmmsearch --tblout OceanDNA-b36597/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb40f1eb3-5017-4355-9322-dc550af35e2f/dqc_reference/reference_markers.hmm OceanDNA-b36597/protein.faa > /dev/null
[2023-03-18 00:54:06,103] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:54:06,103] [INFO] Found 6/6 markers.
[2023-03-18 00:54:06,125] [INFO] Query marker FASTA was written to OceanDNA-b36597/markers.fasta
[2023-03-18 00:54:06,125] [INFO] Task started: Blastn
[2023-03-18 00:54:06,125] [INFO] Running command: blastn -query OceanDNA-b36597/markers.fasta -db /var/lib/cwl/stgb40f1eb3-5017-4355-9322-dc550af35e2f/dqc_reference/reference_markers.fasta -out OceanDNA-b36597/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:54:06,926] [INFO] Task succeeded: Blastn
[2023-03-18 00:54:06,926] [INFO] Selected 14 target genomes.
[2023-03-18 00:54:06,927] [INFO] Target genome list was writen to OceanDNA-b36597/target_genomes.txt
[2023-03-18 00:54:06,931] [INFO] Task started: fastANI
[2023-03-18 00:54:06,931] [INFO] Running command: fastANI --query /var/lib/cwl/stg8258b615-4e3e-4868-99d7-dfe6bcf9c39d/OceanDNA-b36597.fa --refList OceanDNA-b36597/target_genomes.txt --output OceanDNA-b36597/fastani_result.tsv --threads 1
[2023-03-18 00:54:17,246] [INFO] Task succeeded: fastANI
[2023-03-18 00:54:17,246] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb40f1eb3-5017-4355-9322-dc550af35e2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:54:17,247] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb40f1eb3-5017-4355-9322-dc550af35e2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:54:17,255] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:54:17,255] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 00:54:17,256] [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 jadensis	strain=T9	GCA_000756655.1	64988	64988	type	True	87.6887	982	1141	95	below_threshold
Alcanivorax hongdengensis	strain=A-11-3	GCA_000300995.1	519051	519051	type	True	81.3779	683	1141	95	below_threshold
Alcanivorax nanhaiticus	strain=19-m-6	GCA_000756665.1	1177154	1177154	type	True	80.7829	613	1141	95	below_threshold
Alcanivorax profundi	strain=MTEO17	GCA_003597125.1	2338368	2338368	type	True	80.7627	637	1141	95	below_threshold
Alcanivorax sediminis	strain=PA15-N-34	GCA_009601165.1	2663008	2663008	type	True	80.7235	649	1141	95	below_threshold
Alcanivorax borkumensis	strain=SK2	GCA_000009365.1	59754	59754	type	True	79.5282	502	1141	95	below_threshold
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	79.1625	414	1141	95	below_threshold
Alcanivorax venustensis	strain=ISO4	GCA_015356855.1	172371	172371	type	True	79.157	456	1141	95	below_threshold
Alcanivorax dieselolei	strain=CGMCC 1.3690	GCA_014644575.1	285091	285091	type	True	78.5695	410	1141	95	below_threshold
Alcanivorax balearicus	strain=MACL04	GCA_025532145.1	413232	413232	type	True	78.565	398	1141	95	below_threshold
Alcanivorax dieselolei	strain=B5	GCA_000300005.1	285091	285091	type	True	78.524	416	1141	95	below_threshold
Alcanivorax limicola	strain=JB21	GCA_019931215.1	2874102	2874102	type	True	77.7483	248	1141	95	below_threshold
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	76.3574	85	1141	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 00:54:17,256] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36597/tc_result.tsv
[2023-03-18 00:54:17,256] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:54:17,256] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:54:17,256] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb40f1eb3-5017-4355-9322-dc550af35e2f/dqc_reference/checkm_data
[2023-03-18 00:54:17,257] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:54:17,261] [INFO] Task started: CheckM
[2023-03-18 00:54:17,262] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36597/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36597/checkm_input OceanDNA-b36597/checkm_result
[2023-03-18 00:55:11,545] [INFO] Task succeeded: CheckM
[2023-03-18 00:55:11,545] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.10%
Contamintation: 5.21%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 00:55:11,548] [INFO] ===== Completeness check finished =====
[2023-03-18 00:55:11,548] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:55:11,548] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36597/markers.fasta)
[2023-03-18 00:55:11,549] [INFO] Task started: Blastn
[2023-03-18 00:55:11,549] [INFO] Running command: blastn -query OceanDNA-b36597/markers.fasta -db /var/lib/cwl/stgb40f1eb3-5017-4355-9322-dc550af35e2f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36597/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:55:12,988] [INFO] Task succeeded: Blastn
[2023-03-18 00:55:12,988] [INFO] Selected 11 target genomes.
[2023-03-18 00:55:12,988] [INFO] Target genome list was writen to OceanDNA-b36597/target_genomes_gtdb.txt
[2023-03-18 00:55:12,996] [INFO] Task started: fastANI
[2023-03-18 00:55:12,996] [INFO] Running command: fastANI --query /var/lib/cwl/stg8258b615-4e3e-4868-99d7-dfe6bcf9c39d/OceanDNA-b36597.fa --refList OceanDNA-b36597/target_genomes_gtdb.txt --output OceanDNA-b36597/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:55:22,093] [INFO] Task succeeded: fastANI
[2023-03-18 00:55:22,100] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 00:55:22,100] [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_900107995.1	s__Alcanivorax sp900107995	97.9586	1038	1141	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.42	98.03	0.93	0.89	9	conclusive
GCA_014762765.1	s__Alcanivorax sp014762765	89.903	870	1141	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003862375.1	s__Alcanivorax jadensis_A	88.7337	912	1141	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	87.6887	982	1141	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.11	97.73	0.92	0.86	7	-
GCF_000155615.1	s__Alcanivorax sp000155615	81.888	758	1141	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	81.6269	731	1141	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000300995.1	s__Alcanivorax hongdengensis	81.3677	684	1141	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	81.2641	672	1141	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002726155.1	s__Alcanivorax sp002726155	81.1728	718	1141	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	80.7885	611	1141	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009601165.1	s__Alcanivorax sediminis	80.7069	650	1141	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 00:55:22,100] [INFO] GTDB search result was written to OceanDNA-b36597/result_gtdb.tsv
[2023-03-18 00:55:22,100] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:55:22,101] [INFO] DFAST_QC result json was written to OceanDNA-b36597/dqc_result.json
[2023-03-18 00:55:22,102] [INFO] DFAST_QC completed!
[2023-03-18 00:55:22,102] [INFO] Total running time: 0h1m39s