[2023-03-17 03:24:50,922] [INFO] DFAST_QC pipeline started.
[2023-03-17 03:24:50,923] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 03:24:50,923] [INFO] DQC Reference Directory: /var/lib/cwl/stg5335f8cb-787b-411c-855e-91ee57b75280/dqc_reference
[2023-03-17 03:24:52,000] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 03:24:52,000] [INFO] Task started: Prodigal
[2023-03-17 03:24:52,000] [INFO] Running command: cat /var/lib/cwl/stg40050177-eabb-4f41-ac45-18bc3209c703/OceanDNA-b37532.fa | prodigal -d OceanDNA-b37532/cds.fna -a OceanDNA-b37532/protein.faa -g 11 -q > /dev/null
[2023-03-17 03:25:15,346] [INFO] Task succeeded: Prodigal
[2023-03-17 03:25:15,347] [INFO] Task started: HMMsearch
[2023-03-17 03:25:15,347] [INFO] Running command: hmmsearch --tblout OceanDNA-b37532/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5335f8cb-787b-411c-855e-91ee57b75280/dqc_reference/reference_markers.hmm OceanDNA-b37532/protein.faa > /dev/null
[2023-03-17 03:25:15,528] [INFO] Task succeeded: HMMsearch
[2023-03-17 03:25:15,528] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg40050177-eabb-4f41-ac45-18bc3209c703/OceanDNA-b37532.fa]
[2023-03-17 03:25:15,570] [INFO] Query marker FASTA was written to OceanDNA-b37532/markers.fasta
[2023-03-17 03:25:15,571] [INFO] Task started: Blastn
[2023-03-17 03:25:15,572] [INFO] Running command: blastn -query OceanDNA-b37532/markers.fasta -db /var/lib/cwl/stg5335f8cb-787b-411c-855e-91ee57b75280/dqc_reference/reference_markers.fasta -out OceanDNA-b37532/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:25:16,050] [INFO] Task succeeded: Blastn
[2023-03-17 03:25:16,053] [INFO] Selected 11 target genomes.
[2023-03-17 03:25:16,054] [INFO] Target genome list was writen to OceanDNA-b37532/target_genomes.txt
[2023-03-17 03:25:16,060] [INFO] Task started: fastANI
[2023-03-17 03:25:16,060] [INFO] Running command: fastANI --query /var/lib/cwl/stg40050177-eabb-4f41-ac45-18bc3209c703/OceanDNA-b37532.fa --refList OceanDNA-b37532/target_genomes.txt --output OceanDNA-b37532/fastani_result.tsv --threads 1
[2023-03-17 03:25:24,499] [INFO] Task succeeded: fastANI
[2023-03-17 03:25:24,500] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5335f8cb-787b-411c-855e-91ee57b75280/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 03:25:24,500] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5335f8cb-787b-411c-855e-91ee57b75280/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 03:25:24,508] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 03:25:24,508] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 03:25:24,508] [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
Kineobactrum salinum	strain=M2	GCA_010669285.1	2708301	2708301	type	True	79.3342	497	1230	95	below_threshold
Haliea salexigens	strain=DSM 19537	GCA_000423125.1	287487	287487	type	True	78.9132	510	1230	95	below_threshold
Parahaliea aestuarii	strain=S2-26	GCA_008064635.1	1852021	1852021	type	True	78.8883	431	1230	95	below_threshold
Parahaliea mediterranea	strain=DSM 21924	GCA_003402235.1	651086	651086	type	True	78.673	471	1230	95	below_threshold
Parahaliea maris	strain=HSLHS9	GCA_008064665.1	2716870	2716870	type	True	78.4044	419	1230	95	below_threshold
Kineobactrum sediminis	strain=F02	GCA_002868715.1	1905677	1905677	type	True	78.4005	441	1230	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	76.8405	145	1230	95	below_threshold
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	76.7241	143	1230	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	76.7056	142	1230	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	76.5046	121	1230	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	76.4401	123	1230	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 03:25:24,509] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37532/tc_result.tsv
[2023-03-17 03:25:24,510] [INFO] ===== Taxonomy check completed =====
[2023-03-17 03:25:24,510] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 03:25:24,510] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5335f8cb-787b-411c-855e-91ee57b75280/dqc_reference/checkm_data
[2023-03-17 03:25:24,511] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 03:25:24,520] [INFO] Task started: CheckM
[2023-03-17 03:25:24,520] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37532/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37532/checkm_input OceanDNA-b37532/checkm_result
[2023-03-17 03:26:22,045] [INFO] Task succeeded: CheckM
[2023-03-17 03:26:22,045] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 03:26:22,072] [INFO] ===== Completeness check finished =====
[2023-03-17 03:26:22,072] [INFO] ===== Start GTDB Search =====
[2023-03-17 03:26:22,072] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37532/markers.fasta)
[2023-03-17 03:26:22,073] [INFO] Task started: Blastn
[2023-03-17 03:26:22,073] [INFO] Running command: blastn -query OceanDNA-b37532/markers.fasta -db /var/lib/cwl/stg5335f8cb-787b-411c-855e-91ee57b75280/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37532/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:26:22,616] [INFO] Task succeeded: Blastn
[2023-03-17 03:26:22,619] [INFO] Selected 11 target genomes.
[2023-03-17 03:26:22,619] [INFO] Target genome list was writen to OceanDNA-b37532/target_genomes_gtdb.txt
[2023-03-17 03:26:22,694] [INFO] Task started: fastANI
[2023-03-17 03:26:22,694] [INFO] Running command: fastANI --query /var/lib/cwl/stg40050177-eabb-4f41-ac45-18bc3209c703/OceanDNA-b37532.fa --refList OceanDNA-b37532/target_genomes_gtdb.txt --output OceanDNA-b37532/fastani_result_gtdb.tsv --threads 1
[2023-03-17 03:26:31,576] [INFO] Task succeeded: fastANI
[2023-03-17 03:26:31,583] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 03:26:31,583] [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_002692965.1	s__NZNC01 sp002692965	79.3728	513	1230	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__NZNC01	95.0	98.60	97.22	0.91	0.84	3	-
GCF_010669285.1	s__Kineobactrum salinum	79.344	496	1230	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Kineobactrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017255185.1	s__Parahaliea mediterranea_A	79.2718	492	1230	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002416125.1	s__Haliea sp002416125	79.0674	514	1230	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	99.96	99.96	0.96	0.96	2	-
GCF_008064635.1	s__Parahaliea aestuarii	78.8985	430	1230	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423125.1	s__Haliea salexigens	78.8957	512	1230	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	96.91	96.59	0.87	0.83	15	-
GCF_003719295.1	s__Haliea alexandrii	78.8092	492	1230	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003402235.1	s__Parahaliea mediterranea	78.6948	469	1230	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002868715.1	s__Kineobactrum sediminis	78.3972	442	1230	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Kineobactrum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002699145.1	s__Halioglobus sp002699145	78.292	352	1230	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.96	99.96	0.98	0.98	2	-
GCA_009937575.1	s__Halioglobus sp009937575	78.2346	287	1230	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 03:26:31,583] [INFO] GTDB search result was written to OceanDNA-b37532/result_gtdb.tsv
[2023-03-17 03:26:31,583] [INFO] ===== GTDB Search completed =====
[2023-03-17 03:26:31,585] [INFO] DFAST_QC result json was written to OceanDNA-b37532/dqc_result.json
[2023-03-17 03:26:31,585] [INFO] DFAST_QC completed!
[2023-03-17 03:26:31,585] [INFO] Total running time: 0h1m41s