[2023-03-17 23:43:20,540] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:43:20,543] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:43:20,543] [INFO] DQC Reference Directory: /var/lib/cwl/stg4b10502c-3dfc-40f0-8425-61fb3ca4f03d/dqc_reference
[2023-03-17 23:43:21,650] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:43:21,650] [INFO] Task started: Prodigal
[2023-03-17 23:43:21,650] [INFO] Running command: cat /var/lib/cwl/stg148ec551-cb70-4242-a145-ac3ef3f9ffb4/OceanDNA-b24358.fa | prodigal -d OceanDNA-b24358/cds.fna -a OceanDNA-b24358/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:43:27,142] [INFO] Task succeeded: Prodigal
[2023-03-17 23:43:27,143] [INFO] Task started: HMMsearch
[2023-03-17 23:43:27,143] [INFO] Running command: hmmsearch --tblout OceanDNA-b24358/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4b10502c-3dfc-40f0-8425-61fb3ca4f03d/dqc_reference/reference_markers.hmm OceanDNA-b24358/protein.faa > /dev/null
[2023-03-17 23:43:27,295] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:43:27,295] [INFO] Found 6/6 markers.
[2023-03-17 23:43:27,328] [INFO] Query marker FASTA was written to OceanDNA-b24358/markers.fasta
[2023-03-17 23:43:27,329] [INFO] Task started: Blastn
[2023-03-17 23:43:27,329] [INFO] Running command: blastn -query OceanDNA-b24358/markers.fasta -db /var/lib/cwl/stg4b10502c-3dfc-40f0-8425-61fb3ca4f03d/dqc_reference/reference_markers.fasta -out OceanDNA-b24358/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:43:27,872] [INFO] Task succeeded: Blastn
[2023-03-17 23:43:27,872] [INFO] Selected 19 target genomes.
[2023-03-17 23:43:27,873] [INFO] Target genome list was writen to OceanDNA-b24358/target_genomes.txt
[2023-03-17 23:43:27,887] [INFO] Task started: fastANI
[2023-03-17 23:43:27,887] [INFO] Running command: fastANI --query /var/lib/cwl/stg148ec551-cb70-4242-a145-ac3ef3f9ffb4/OceanDNA-b24358.fa --refList OceanDNA-b24358/target_genomes.txt --output OceanDNA-b24358/fastani_result.tsv --threads 1
[2023-03-17 23:43:35,931] [INFO] Task succeeded: fastANI
[2023-03-17 23:43:35,931] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4b10502c-3dfc-40f0-8425-61fb3ca4f03d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:43:35,932] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4b10502c-3dfc-40f0-8425-61fb3ca4f03d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:43:35,932] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:43:35,932] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 23:43:35,932] [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
--------------------------------------------------------------------------------
[2023-03-17 23:43:35,934] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24358/tc_result.tsv
[2023-03-17 23:43:35,936] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:43:35,936] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:43:35,936] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4b10502c-3dfc-40f0-8425-61fb3ca4f03d/dqc_reference/checkm_data
[2023-03-17 23:43:35,939] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:43:35,941] [INFO] Task started: CheckM
[2023-03-17 23:43:35,941] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24358/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24358/checkm_input OceanDNA-b24358/checkm_result
[2023-03-17 23:43:55,442] [INFO] Task succeeded: CheckM
[2023-03-17 23:43:55,442] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.22%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 23:43:55,444] [INFO] ===== Completeness check finished =====
[2023-03-17 23:43:55,444] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:43:55,444] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24358/markers.fasta)
[2023-03-17 23:43:55,445] [INFO] Task started: Blastn
[2023-03-17 23:43:55,445] [INFO] Running command: blastn -query OceanDNA-b24358/markers.fasta -db /var/lib/cwl/stg4b10502c-3dfc-40f0-8425-61fb3ca4f03d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24358/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:43:56,360] [INFO] Task succeeded: Blastn
[2023-03-17 23:43:56,362] [INFO] Selected 34 target genomes.
[2023-03-17 23:43:56,362] [INFO] Target genome list was writen to OceanDNA-b24358/target_genomes_gtdb.txt
[2023-03-17 23:43:56,461] [INFO] Task started: fastANI
[2023-03-17 23:43:56,461] [INFO] Running command: fastANI --query /var/lib/cwl/stg148ec551-cb70-4242-a145-ac3ef3f9ffb4/OceanDNA-b24358.fa --refList OceanDNA-b24358/target_genomes_gtdb.txt --output OceanDNA-b24358/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:44:03,440] [INFO] Task succeeded: fastANI
[2023-03-17 23:44:03,450] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 23:44:03,450] [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_902577425.1	s__MarineAlpha5-Bin3 sp902577425	76.6622	92	282	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__MarineAlpha5-Bin3	95.0	95.54	95.54	0.86	0.86	2	-
GCA_002938205.1	s__AG-337-I02 sp002938205	76.5184	54	282	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	99.93	99.93	0.95	0.95	2	-
GCA_017639935.1	s__JAGFWP01 sp017639935	76.4681	50	282	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__JAGFWP01	95.0	99.64	99.12	0.86	0.76	8	-
GCA_902567855.1	s__MarineAlpha5-Bin3 sp902567855	76.3972	82	282	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__MarineAlpha5-Bin3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902553945.1	s__AG-337-I02 sp902553945	76.3362	54	282	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902567135.1	s__AG-337-I02 sp902567135	76.3105	53	282	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902635455.1	s__CACPNW01 sp902635455	76.2132	50	282	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__CACPNW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902576125.1	s__AG-337-I02 sp902576125	76.1898	56	282	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902602515.1	s__AG-337-I02 sp902602515	76.1572	51	282	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	99.95	99.95	0.92	0.92	2	-
GCA_902591485.1	s__AG-337-I02 sp902591485	76.1557	53	282	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	97.00	97.00	0.77	0.77	2	-
GCA_902512325.1	s__AG-337-I02 sp902512325	76.0567	61	282	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902525035.1	s__AG-337-I02 sp902525035	75.9696	51	282	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902560725.1	s__AG-337-I02 sp902560725	75.9379	60	282	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902521315.1	s__AG-337-I02 sp902521315	75.9025	55	282	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902623255.1	s__AG-337-I02 sp902623255	75.8657	55	282	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902614085.1	s__AG-337-I02 sp902614085	75.8357	59	282	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902560675.1	s__AG-337-I02 sp902554185	75.6277	52	282	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	98.99	98.59	0.82	0.79	4	-
GCA_902596365.1	s__AG-337-I02 sp902596365	75.5943	51	282	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 23:44:03,461] [INFO] GTDB search result was written to OceanDNA-b24358/result_gtdb.tsv
[2023-03-17 23:44:03,462] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:44:03,463] [INFO] DFAST_QC result json was written to OceanDNA-b24358/dqc_result.json
[2023-03-17 23:44:03,463] [INFO] DFAST_QC completed!
[2023-03-17 23:44:03,463] [INFO] Total running time: 0h0m43s