[2023-03-15 15:18:22,058] [INFO] DFAST_QC pipeline started.
[2023-03-15 15:18:22,059] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 15:18:22,059] [INFO] DQC Reference Directory: /var/lib/cwl/stg58848617-6eb9-476f-b053-9acc85f708d4/dqc_reference
[2023-03-15 15:18:23,188] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 15:18:23,188] [INFO] Task started: Prodigal
[2023-03-15 15:18:23,188] [INFO] Running command: cat /var/lib/cwl/stg3f7697ce-fac0-45dc-acf2-e3ea6b7e28ee/OceanDNA-b34310.fa | prodigal -d OceanDNA-b34310/cds.fna -a OceanDNA-b34310/protein.faa -g 11 -q > /dev/null
[2023-03-15 15:18:46,039] [INFO] Task succeeded: Prodigal
[2023-03-15 15:18:46,039] [INFO] Task started: HMMsearch
[2023-03-15 15:18:46,039] [INFO] Running command: hmmsearch --tblout OceanDNA-b34310/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg58848617-6eb9-476f-b053-9acc85f708d4/dqc_reference/reference_markers.hmm OceanDNA-b34310/protein.faa > /dev/null
[2023-03-15 15:18:46,293] [INFO] Task succeeded: HMMsearch
[2023-03-15 15:18:46,293] [INFO] Found 6/6 markers.
[2023-03-15 15:18:46,347] [INFO] Query marker FASTA was written to OceanDNA-b34310/markers.fasta
[2023-03-15 15:18:46,347] [INFO] Task started: Blastn
[2023-03-15 15:18:46,347] [INFO] Running command: blastn -query OceanDNA-b34310/markers.fasta -db /var/lib/cwl/stg58848617-6eb9-476f-b053-9acc85f708d4/dqc_reference/reference_markers.fasta -out OceanDNA-b34310/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:18:47,023] [INFO] Task succeeded: Blastn
[2023-03-15 15:18:47,028] [INFO] Selected 14 target genomes.
[2023-03-15 15:18:47,029] [INFO] Target genome list was writen to OceanDNA-b34310/target_genomes.txt
[2023-03-15 15:18:47,041] [INFO] Task started: fastANI
[2023-03-15 15:18:47,041] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f7697ce-fac0-45dc-acf2-e3ea6b7e28ee/OceanDNA-b34310.fa --refList OceanDNA-b34310/target_genomes.txt --output OceanDNA-b34310/fastani_result.tsv --threads 1
[2023-03-15 15:18:59,590] [INFO] Task succeeded: fastANI
[2023-03-15 15:18:59,591] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg58848617-6eb9-476f-b053-9acc85f708d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 15:18:59,591] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg58848617-6eb9-476f-b053-9acc85f708d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 15:18:59,598] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2023-03-15 15:18:59,598] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 15:18:59,598] [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
Alteromonas abrolhosensis	strain=PEL67E	GCA_001953635.1	1892904	1892904	type	True	97.6086	1237	1371	95	conclusive
Alteromonas macleodii	strain=ATCC 27126	GCA_000172635.2	28108	28108	type	True	90.1572	1126	1371	95	below_threshold
Alteromonas portus	strain=HB161718	GCA_005117025.1	2565549	2565549	type	True	86.5737	962	1371	95	below_threshold
Alteromonas mediterranea	strain=DE	GCA_000020585.3	314275	314275	type	True	83.5821	850	1371	95	below_threshold
Alteromonas gracilis	strain=9a2	GCA_002993325.1	1479524	1479524	type	True	83.4042	863	1371	95	below_threshold
Alteromonas australica	strain=H 17	GCA_000730385.1	589873	589873	type	True	80.6274	369	1371	95	below_threshold
Alteromonas naphthalenivorans	strain=SN2	GCA_000213655.1	715451	715451	type	True	79.5453	378	1371	95	below_threshold
Psychrosphaera ytuae	strain=MTZ26	GCA_017638545.1	2820710	2820710	type	True	77.337	50	1371	95	below_threshold
Photobacterium sanguinicancri	strain=CECT 7579	GCA_024346675.1	875932	875932	type	True	76.5607	51	1371	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 15:18:59,600] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34310/tc_result.tsv
[2023-03-15 15:18:59,601] [INFO] ===== Taxonomy check completed =====
[2023-03-15 15:18:59,601] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 15:18:59,601] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg58848617-6eb9-476f-b053-9acc85f708d4/dqc_reference/checkm_data
[2023-03-15 15:18:59,602] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 15:18:59,639] [INFO] Task started: CheckM
[2023-03-15 15:18:59,639] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34310/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34310/checkm_input OceanDNA-b34310/checkm_result
[2023-03-15 15:19:56,796] [INFO] Task succeeded: CheckM
[2023-03-15 15:19:56,797] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 15:19:56,849] [INFO] ===== Completeness check finished =====
[2023-03-15 15:19:56,849] [INFO] ===== Start GTDB Search =====
[2023-03-15 15:19:56,850] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34310/markers.fasta)
[2023-03-15 15:19:56,851] [INFO] Task started: Blastn
[2023-03-15 15:19:56,851] [INFO] Running command: blastn -query OceanDNA-b34310/markers.fasta -db /var/lib/cwl/stg58848617-6eb9-476f-b053-9acc85f708d4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34310/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:19:57,916] [INFO] Task succeeded: Blastn
[2023-03-15 15:19:57,931] [INFO] Selected 9 target genomes.
[2023-03-15 15:19:57,931] [INFO] Target genome list was writen to OceanDNA-b34310/target_genomes_gtdb.txt
[2023-03-15 15:19:57,936] [INFO] Task started: fastANI
[2023-03-15 15:19:57,936] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f7697ce-fac0-45dc-acf2-e3ea6b7e28ee/OceanDNA-b34310.fa --refList OceanDNA-b34310/target_genomes_gtdb.txt --output OceanDNA-b34310/fastani_result_gtdb.tsv --threads 1
[2023-03-15 15:20:06,957] [INFO] Task succeeded: fastANI
[2023-03-15 15:20:06,963] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 15:20:06,964] [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_001953635.1	s__Alteromonas abrolhosensis	97.6086	1237	1371	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.27	97.25	0.92	0.89	10	conclusive
GCF_000172635.2	s__Alteromonas macleodii	90.1576	1127	1371	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.79	96.10	0.88	0.76	56	-
GCF_000808575.1	s__Alteromonas marina	89.0211	1013	1371	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.44	97.44	0.91	0.91	2	-
GCF_005117025.1	s__Alteromonas portus	86.5737	962	1371	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001885075.1	s__Alteromonas sp001885075	85.0192	708	1371	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903772925.1	s__Alteromonas macleodii_A	84.5185	943	1371	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003443615.1	s__Alteromonas sp003443615	84.0929	949	1371	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000597705.1	s__Alteromonas sp000597705	83.982	958	1371	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.20	99.20	0.96	0.96	2	-
GCF_000020585.3	s__Alteromonas mediterranea	83.5756	850	1371	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.15	97.41	0.86	0.82	24	-
--------------------------------------------------------------------------------
[2023-03-15 15:20:06,968] [INFO] GTDB search result was written to OceanDNA-b34310/result_gtdb.tsv
[2023-03-15 15:20:06,976] [INFO] ===== GTDB Search completed =====
[2023-03-15 15:20:06,984] [INFO] DFAST_QC result json was written to OceanDNA-b34310/dqc_result.json
[2023-03-15 15:20:06,984] [INFO] DFAST_QC completed!
[2023-03-15 15:20:06,984] [INFO] Total running time: 0h1m45s