[2023-03-19 00:29:45,952] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:29:45,953] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:29:45,953] [INFO] DQC Reference Directory: /var/lib/cwl/stgfc5ea343-e544-47e3-9bf7-b7bab035a266/dqc_reference
[2023-03-19 00:29:47,081] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:29:47,081] [INFO] Task started: Prodigal
[2023-03-19 00:29:47,081] [INFO] Running command: cat /var/lib/cwl/stg004f9d2e-bb47-4955-9295-558f76b10339/OceanDNA-b23603.fa | prodigal -d OceanDNA-b23603/cds.fna -a OceanDNA-b23603/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:30:03,904] [INFO] Task succeeded: Prodigal
[2023-03-19 00:30:03,904] [INFO] Task started: HMMsearch
[2023-03-19 00:30:03,904] [INFO] Running command: hmmsearch --tblout OceanDNA-b23603/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfc5ea343-e544-47e3-9bf7-b7bab035a266/dqc_reference/reference_markers.hmm OceanDNA-b23603/protein.faa > /dev/null
[2023-03-19 00:30:04,089] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:30:04,090] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg004f9d2e-bb47-4955-9295-558f76b10339/OceanDNA-b23603.fa]
[2023-03-19 00:30:04,110] [INFO] Query marker FASTA was written to OceanDNA-b23603/markers.fasta
[2023-03-19 00:30:04,111] [INFO] Task started: Blastn
[2023-03-19 00:30:04,111] [INFO] Running command: blastn -query OceanDNA-b23603/markers.fasta -db /var/lib/cwl/stgfc5ea343-e544-47e3-9bf7-b7bab035a266/dqc_reference/reference_markers.fasta -out OceanDNA-b23603/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:30:04,765] [INFO] Task succeeded: Blastn
[2023-03-19 00:30:04,766] [INFO] Selected 11 target genomes.
[2023-03-19 00:30:04,766] [INFO] Target genome list was writen to OceanDNA-b23603/target_genomes.txt
[2023-03-19 00:30:04,773] [INFO] Task started: fastANI
[2023-03-19 00:30:04,773] [INFO] Running command: fastANI --query /var/lib/cwl/stg004f9d2e-bb47-4955-9295-558f76b10339/OceanDNA-b23603.fa --refList OceanDNA-b23603/target_genomes.txt --output OceanDNA-b23603/fastani_result.tsv --threads 1
[2023-03-19 00:30:12,530] [INFO] Task succeeded: fastANI
[2023-03-19 00:30:12,530] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfc5ea343-e544-47e3-9bf7-b7bab035a266/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:30:12,531] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfc5ea343-e544-47e3-9bf7-b7bab035a266/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:30:12,537] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:30:12,537] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 00:30:12,538] [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
Hyphomonas chukchiensis	strain=BH-BN04-4	GCA_000682695.1	1280947	1280947	type	True	82.0848	626	881	95	below_threshold
Hyphomonas johnsonii	strain=MHS-2	GCA_000685275.1	81031	81031	type	True	82.0826	603	881	95	below_threshold
Hyphomonas oceanitis	strain=SCH89	GCA_000685295.1	81033	81033	type	True	81.9053	603	881	95	below_threshold
Hyphomonas jannaschiana	strain=VP2	GCA_000685215.1	86	86	type	True	78.4947	363	881	95	below_threshold
Hyphomonas adhaerens	strain=MHS-3	GCA_000685235.1	81029	81029	type	True	78.3904	353	881	95	below_threshold
Hyphomonas polymorpha	strain=PS728	GCA_000685315.1	74319	74319	type	True	78.0235	270	881	95	below_threshold
Hyphomonas sediminis	strain=WL0036	GCA_019679475.1	2866160	2866160	type	True	77.5418	256	881	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	75.643	58	881	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	75.4525	58	881	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 00:30:12,538] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23603/tc_result.tsv
[2023-03-19 00:30:12,538] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:30:12,538] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:30:12,538] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfc5ea343-e544-47e3-9bf7-b7bab035a266/dqc_reference/checkm_data
[2023-03-19 00:30:12,539] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:30:12,573] [INFO] Task started: CheckM
[2023-03-19 00:30:12,574] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23603/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23603/checkm_input OceanDNA-b23603/checkm_result
[2023-03-19 00:30:56,594] [INFO] Task succeeded: CheckM
[2023-03-19 00:30:56,594] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.03%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:30:56,596] [INFO] ===== Completeness check finished =====
[2023-03-19 00:30:56,596] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:30:56,597] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23603/markers.fasta)
[2023-03-19 00:30:56,597] [INFO] Task started: Blastn
[2023-03-19 00:30:56,597] [INFO] Running command: blastn -query OceanDNA-b23603/markers.fasta -db /var/lib/cwl/stgfc5ea343-e544-47e3-9bf7-b7bab035a266/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23603/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:30:57,750] [INFO] Task succeeded: Blastn
[2023-03-19 00:30:57,751] [INFO] Selected 7 target genomes.
[2023-03-19 00:30:57,751] [INFO] Target genome list was writen to OceanDNA-b23603/target_genomes_gtdb.txt
[2023-03-19 00:30:57,761] [INFO] Task started: fastANI
[2023-03-19 00:30:57,761] [INFO] Running command: fastANI --query /var/lib/cwl/stg004f9d2e-bb47-4955-9295-558f76b10339/OceanDNA-b23603.fa --refList OceanDNA-b23603/target_genomes_gtdb.txt --output OceanDNA-b23603/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:31:03,360] [INFO] Task succeeded: fastANI
[2023-03-19 00:31:03,365] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 00:31:03,365] [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_018830285.1	s__Hyphomonas sp018830285	90.2794	740	881	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000961795.1	s__Hyphomonas sp000961795	82.8372	617	881	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000682695.1	s__Hyphomonas chukchiensis	82.0848	626	881	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000685275.1	s__Hyphomonas johnsonii	82.0833	603	881	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000685295.1	s__Hyphomonas oceanitis	81.9053	603	881	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018827375.1	s__Hyphomonas sp018827375	81.3125	596	881	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.92	99.88	0.98	0.97	4	-
--------------------------------------------------------------------------------
[2023-03-19 00:31:03,365] [INFO] GTDB search result was written to OceanDNA-b23603/result_gtdb.tsv
[2023-03-19 00:31:03,365] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:31:03,366] [INFO] DFAST_QC result json was written to OceanDNA-b23603/dqc_result.json
[2023-03-19 00:31:03,367] [INFO] DFAST_QC completed!
[2023-03-19 00:31:03,367] [INFO] Total running time: 0h1m17s