[2023-03-16 07:15:38,903] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:15:38,903] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:15:38,903] [INFO] DQC Reference Directory: /var/lib/cwl/stg3687bce0-aa03-47c2-ba58-f52feb36af63/dqc_reference
[2023-03-16 07:15:39,971] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:15:39,972] [INFO] Task started: Prodigal
[2023-03-16 07:15:39,972] [INFO] Running command: cat /var/lib/cwl/stg44366491-5f4d-41f0-ac50-c64ea1ff7ac1/OceanDNA-b9784.fa | prodigal -d OceanDNA-b9784/cds.fna -a OceanDNA-b9784/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:16:08,583] [INFO] Task succeeded: Prodigal
[2023-03-16 07:16:08,584] [INFO] Task started: HMMsearch
[2023-03-16 07:16:08,584] [INFO] Running command: hmmsearch --tblout OceanDNA-b9784/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3687bce0-aa03-47c2-ba58-f52feb36af63/dqc_reference/reference_markers.hmm OceanDNA-b9784/protein.faa > /dev/null
[2023-03-16 07:16:08,795] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:16:08,795] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg44366491-5f4d-41f0-ac50-c64ea1ff7ac1/OceanDNA-b9784.fa]
[2023-03-16 07:16:08,818] [INFO] Query marker FASTA was written to OceanDNA-b9784/markers.fasta
[2023-03-16 07:16:08,820] [INFO] Task started: Blastn
[2023-03-16 07:16:08,820] [INFO] Running command: blastn -query OceanDNA-b9784/markers.fasta -db /var/lib/cwl/stg3687bce0-aa03-47c2-ba58-f52feb36af63/dqc_reference/reference_markers.fasta -out OceanDNA-b9784/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:16:09,371] [INFO] Task succeeded: Blastn
[2023-03-16 07:16:09,372] [INFO] Selected 10 target genomes.
[2023-03-16 07:16:09,372] [INFO] Target genome list was writen to OceanDNA-b9784/target_genomes.txt
[2023-03-16 07:16:09,379] [INFO] Task started: fastANI
[2023-03-16 07:16:09,379] [INFO] Running command: fastANI --query /var/lib/cwl/stg44366491-5f4d-41f0-ac50-c64ea1ff7ac1/OceanDNA-b9784.fa --refList OceanDNA-b9784/target_genomes.txt --output OceanDNA-b9784/fastani_result.tsv --threads 1
[2023-03-16 07:16:17,274] [INFO] Task succeeded: fastANI
[2023-03-16 07:16:17,275] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3687bce0-aa03-47c2-ba58-f52feb36af63/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:16:17,275] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3687bce0-aa03-47c2-ba58-f52feb36af63/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:16:17,281] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2023-03-16 07:16:17,281] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-16 07:16:17,281] [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
Muricauda aurea	strain=BC31-1-A7	GCA_017313785.1	2915619	2915619	type	True	99.2078	1059	1134	95	conclusive
Muricauda brasiliensis	strain=K001	GCA_003057865.1	2162892	2162892	type	True	89.7617	910	1134	95	below_threshold
Muricauda chongwuensis	strain=HICW	GCA_013376415.1	2697365	2697365	type	True	89.732	876	1134	95	below_threshold
Muricauda oceani	strain=501str8	GCA_019457985.1	2698672	2698672	type	True	85.061	806	1134	95	below_threshold
Muricauda oceani	strain=501str8	GCA_011068285.1	2698672	2698672	type	True	84.9917	819	1134	95	below_threshold
Muricauda oceanensis	strain=40DY170	GCA_003992595.1	2499163	2499163	type	True	82.5873	757	1134	95	below_threshold
Muricauda profundi	strain=BC31-3-A3	GCA_017313275.1	2915620	2915620	type	True	82.3151	661	1134	95	below_threshold
Muricauda hadalis	strain=MT-229	GCA_007785775.2	2597517	2597517	type	True	79.4007	445	1134	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 07:16:17,281] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9784/tc_result.tsv
[2023-03-16 07:16:17,282] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:16:17,282] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:16:17,282] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3687bce0-aa03-47c2-ba58-f52feb36af63/dqc_reference/checkm_data
[2023-03-16 07:16:17,282] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:16:17,287] [INFO] Task started: CheckM
[2023-03-16 07:16:17,287] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9784/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9784/checkm_input OceanDNA-b9784/checkm_result
[2023-03-16 07:17:28,004] [INFO] Task succeeded: CheckM
[2023-03-16 07:17:28,004] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.86%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 07:17:28,007] [INFO] ===== Completeness check finished =====
[2023-03-16 07:17:28,007] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:17:28,007] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9784/markers.fasta)
[2023-03-16 07:17:28,008] [INFO] Task started: Blastn
[2023-03-16 07:17:28,008] [INFO] Running command: blastn -query OceanDNA-b9784/markers.fasta -db /var/lib/cwl/stg3687bce0-aa03-47c2-ba58-f52feb36af63/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9784/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:17:28,748] [INFO] Task succeeded: Blastn
[2023-03-16 07:17:28,748] [INFO] Selected 11 target genomes.
[2023-03-16 07:17:28,748] [INFO] Target genome list was writen to OceanDNA-b9784/target_genomes_gtdb.txt
[2023-03-16 07:17:28,758] [INFO] Task started: fastANI
[2023-03-16 07:17:28,758] [INFO] Running command: fastANI --query /var/lib/cwl/stg44366491-5f4d-41f0-ac50-c64ea1ff7ac1/OceanDNA-b9784.fa --refList OceanDNA-b9784/target_genomes_gtdb.txt --output OceanDNA-b9784/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:17:38,066] [INFO] Task succeeded: fastANI
[2023-03-16 07:17:38,073] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 07:17:38,073] [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_017313785.1	s__Muricauda sp002711825	99.2078	1059	1134	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	98.76	98.31	0.81	0.77	4	conclusive
GCF_003057865.1	s__Muricauda brasiliensis	89.7617	910	1134	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	96.90	96.90	0.89	0.89	2	-
GCF_011068285.1	s__Muricauda sp011068285	84.9915	819	1134	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010468565.1	s__Muricauda sp010468565	82.9222	721	1134	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003992595.1	s__Muricauda sp002452975	82.5904	756	1134	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	99.01	99.01	0.89	0.89	2	-
GCF_017313275.1	s__Muricauda lutimaris_A	82.2957	663	1134	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911645.1	s__Muricauda sp013911645	81.9427	688	1134	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017313105.1	s__Muricauda sp017313105	81.7819	636	1134	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000224085.1	s__Muricauda ruestringensis	81.3219	696	1134	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002167435.2	s__Muricauda sp002167435	81.1116	574	1134	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222835.1	s__Muricauda sp018222835	80.4835	527	1134	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 07:17:38,074] [INFO] GTDB search result was written to OceanDNA-b9784/result_gtdb.tsv
[2023-03-16 07:17:38,074] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:17:38,075] [INFO] DFAST_QC result json was written to OceanDNA-b9784/dqc_result.json
[2023-03-16 07:17:38,075] [INFO] DFAST_QC completed!
[2023-03-16 07:17:38,076] [INFO] Total running time: 0h1m59s