[2023-03-15 13:54:06,236] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:54:06,236] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:54:06,236] [INFO] DQC Reference Directory: /var/lib/cwl/stge87bf177-ea78-44c9-ace0-a38b844b3ebb/dqc_reference
[2023-03-15 13:54:07,325] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:54:07,326] [INFO] Task started: Prodigal
[2023-03-15 13:54:07,326] [INFO] Running command: cat /var/lib/cwl/stg83b8c857-769e-4d9c-94fe-c311b8360d22/OceanDNA-b18365.fa | prodigal -d OceanDNA-b18365/cds.fna -a OceanDNA-b18365/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:54:10,700] [INFO] Task succeeded: Prodigal
[2023-03-15 13:54:10,700] [INFO] Task started: HMMsearch
[2023-03-15 13:54:10,700] [INFO] Running command: hmmsearch --tblout OceanDNA-b18365/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge87bf177-ea78-44c9-ace0-a38b844b3ebb/dqc_reference/reference_markers.hmm OceanDNA-b18365/protein.faa > /dev/null
[2023-03-15 13:54:10,894] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:54:10,895] [INFO] Found 6/6 markers.
[2023-03-15 13:54:10,921] [INFO] Query marker FASTA was written to OceanDNA-b18365/markers.fasta
[2023-03-15 13:54:10,921] [INFO] Task started: Blastn
[2023-03-15 13:54:10,922] [INFO] Running command: blastn -query OceanDNA-b18365/markers.fasta -db /var/lib/cwl/stge87bf177-ea78-44c9-ace0-a38b844b3ebb/dqc_reference/reference_markers.fasta -out OceanDNA-b18365/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:54:11,475] [INFO] Task succeeded: Blastn
[2023-03-15 13:54:11,479] [INFO] Selected 21 target genomes.
[2023-03-15 13:54:11,479] [INFO] Target genome list was writen to OceanDNA-b18365/target_genomes.txt
[2023-03-15 13:54:11,490] [INFO] Task started: fastANI
[2023-03-15 13:54:11,490] [INFO] Running command: fastANI --query /var/lib/cwl/stg83b8c857-769e-4d9c-94fe-c311b8360d22/OceanDNA-b18365.fa --refList OceanDNA-b18365/target_genomes.txt --output OceanDNA-b18365/fastani_result.tsv --threads 1
[2023-03-15 13:54:22,543] [INFO] Task succeeded: fastANI
[2023-03-15 13:54:22,543] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge87bf177-ea78-44c9-ace0-a38b844b3ebb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:54:22,543] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge87bf177-ea78-44c9-ace0-a38b844b3ebb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:54:22,544] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:54:22,544] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 13:54:22,544] [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
--------------------------------------------------------------------------------
[2023-03-15 13:54:22,546] [INFO] DFAST Taxonomy check result was written to OceanDNA-b18365/tc_result.tsv
[2023-03-15 13:54:22,549] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:54:22,549] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:54:22,549] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge87bf177-ea78-44c9-ace0-a38b844b3ebb/dqc_reference/checkm_data
[2023-03-15 13:54:22,553] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:54:22,556] [INFO] Task started: CheckM
[2023-03-15 13:54:22,556] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b18365/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b18365/checkm_input OceanDNA-b18365/checkm_result
[2023-03-15 13:54:38,292] [INFO] Task succeeded: CheckM
[2023-03-15 13:54:38,293] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.63%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 13:54:38,322] [INFO] ===== Completeness check finished =====
[2023-03-15 13:54:38,323] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:54:38,323] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b18365/markers.fasta)
[2023-03-15 13:54:38,324] [INFO] Task started: Blastn
[2023-03-15 13:54:38,324] [INFO] Running command: blastn -query OceanDNA-b18365/markers.fasta -db /var/lib/cwl/stge87bf177-ea78-44c9-ace0-a38b844b3ebb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b18365/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:54:39,127] [INFO] Task succeeded: Blastn
[2023-03-15 13:54:39,134] [INFO] Selected 10 target genomes.
[2023-03-15 13:54:39,134] [INFO] Target genome list was writen to OceanDNA-b18365/target_genomes_gtdb.txt
[2023-03-15 13:54:39,138] [INFO] Task started: fastANI
[2023-03-15 13:54:39,138] [INFO] Running command: fastANI --query /var/lib/cwl/stg83b8c857-769e-4d9c-94fe-c311b8360d22/OceanDNA-b18365.fa --refList OceanDNA-b18365/target_genomes_gtdb.txt --output OceanDNA-b18365/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:54:40,576] [INFO] Task succeeded: fastANI
[2023-03-15 13:54:40,582] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 13:54:40,583] [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_902578385.1	s__Marinisoma sp002710515	98.3507	194	211	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	97.88	96.56	0.86	0.83	7	conclusive
GCA_902599655.1	s__Marinisoma sp902599655	83.5309	144	211	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	97.53	97.28	0.66	0.66	3	-
GCA_016777965.1	s__Marinisoma sp016777965	83.3981	76	211	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902526795.1	s__Marinisoma sp902526795	83.3819	173	211	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902576865.1	s__Marinisoma sp902576865	83.2256	135	211	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	96.64	96.64	0.80	0.80	2	-
GCA_902538565.1	s__Marinisoma sp902538565	82.9026	188	211	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	99.07	99.04	0.96	0.96	3	-
GCA_902525615.1	s__Marinisoma sp902525615	82.8358	161	211	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000402655.1	s__Marinisoma sp000402655	82.7126	182	211	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	96.42	95.83	0.93	0.92	4	-
GCA_902624275.1	s__Marinisoma sp902624275	82.3425	162	211	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902624575.1	s__Marinisoma sp902624575	78.7982	72	211	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 13:54:40,584] [INFO] GTDB search result was written to OceanDNA-b18365/result_gtdb.tsv
[2023-03-15 13:54:40,584] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:54:40,587] [INFO] DFAST_QC result json was written to OceanDNA-b18365/dqc_result.json
[2023-03-15 13:54:40,587] [INFO] DFAST_QC completed!
[2023-03-15 13:54:40,587] [INFO] Total running time: 0h0m34s