[2023-03-18 00:35:06,624] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:35:06,624] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:35:06,625] [INFO] DQC Reference Directory: /var/lib/cwl/stg08a67f59-40da-42bd-9d3d-dec95e032b1f/dqc_reference
[2023-03-18 00:35:07,858] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:35:07,858] [INFO] Task started: Prodigal
[2023-03-18 00:35:07,859] [INFO] Running command: cat /var/lib/cwl/stg5f4df5fc-590c-482b-a4ef-bdf9c34a0948/OceanDNA-b13566.fa | prodigal -d OceanDNA-b13566/cds.fna -a OceanDNA-b13566/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:35:28,367] [INFO] Task succeeded: Prodigal
[2023-03-18 00:35:28,367] [INFO] Task started: HMMsearch
[2023-03-18 00:35:28,367] [INFO] Running command: hmmsearch --tblout OceanDNA-b13566/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg08a67f59-40da-42bd-9d3d-dec95e032b1f/dqc_reference/reference_markers.hmm OceanDNA-b13566/protein.faa > /dev/null
[2023-03-18 00:35:28,662] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:35:28,663] [INFO] Found 6/6 markers.
[2023-03-18 00:35:28,687] [INFO] Query marker FASTA was written to OceanDNA-b13566/markers.fasta
[2023-03-18 00:35:28,687] [INFO] Task started: Blastn
[2023-03-18 00:35:28,687] [INFO] Running command: blastn -query OceanDNA-b13566/markers.fasta -db /var/lib/cwl/stg08a67f59-40da-42bd-9d3d-dec95e032b1f/dqc_reference/reference_markers.fasta -out OceanDNA-b13566/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:35:29,209] [INFO] Task succeeded: Blastn
[2023-03-18 00:35:29,209] [INFO] Selected 16 target genomes.
[2023-03-18 00:35:29,210] [INFO] Target genome list was writen to OceanDNA-b13566/target_genomes.txt
[2023-03-18 00:35:29,218] [INFO] Task started: fastANI
[2023-03-18 00:35:29,218] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f4df5fc-590c-482b-a4ef-bdf9c34a0948/OceanDNA-b13566.fa --refList OceanDNA-b13566/target_genomes.txt --output OceanDNA-b13566/fastani_result.tsv --threads 1
[2023-03-18 00:35:37,701] [INFO] Task succeeded: fastANI
[2023-03-18 00:35:37,702] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg08a67f59-40da-42bd-9d3d-dec95e032b1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:35:37,702] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg08a67f59-40da-42bd-9d3d-dec95e032b1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:35:37,702] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:35:37,702] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 00:35:37,702] [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
--------------------------------------------------------------------------------
[2023-03-18 00:35:37,702] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13566/tc_result.tsv
[2023-03-18 00:35:37,702] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:35:37,702] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:35:37,703] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg08a67f59-40da-42bd-9d3d-dec95e032b1f/dqc_reference/checkm_data
[2023-03-18 00:35:37,705] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:35:37,711] [INFO] Task started: CheckM
[2023-03-18 00:35:37,711] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13566/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13566/checkm_input OceanDNA-b13566/checkm_result
[2023-03-18 00:36:30,217] [INFO] Task succeeded: CheckM
[2023-03-18 00:36:30,218] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.40%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 00:36:30,222] [INFO] ===== Completeness check finished =====
[2023-03-18 00:36:30,222] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:36:30,222] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13566/markers.fasta)
[2023-03-18 00:36:30,222] [INFO] Task started: Blastn
[2023-03-18 00:36:30,222] [INFO] Running command: blastn -query OceanDNA-b13566/markers.fasta -db /var/lib/cwl/stg08a67f59-40da-42bd-9d3d-dec95e032b1f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13566/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:36:30,908] [INFO] Task succeeded: Blastn
[2023-03-18 00:36:30,909] [INFO] Selected 21 target genomes.
[2023-03-18 00:36:30,909] [INFO] Target genome list was writen to OceanDNA-b13566/target_genomes_gtdb.txt
[2023-03-18 00:36:30,932] [INFO] Task started: fastANI
[2023-03-18 00:36:30,932] [INFO] Running command: fastANI --query /var/lib/cwl/stg5f4df5fc-590c-482b-a4ef-bdf9c34a0948/OceanDNA-b13566.fa --refList OceanDNA-b13566/target_genomes_gtdb.txt --output OceanDNA-b13566/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:36:42,370] [INFO] Task succeeded: fastANI
[2023-03-18 00:36:42,375] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 00:36:42,375] [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_018648685.1	s__Desulfolinea sp018648685	99.6301	861	1180	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__Desulfolinea	95.0	99.60	99.55	0.84	0.83	3	conclusive
GCA_018648655.1	s__Desulfolinea sp018648655	80.2906	297	1180	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__Desulfolinea	95.0	99.77	99.77	0.84	0.82	3	-
GCA_018648605.1	s__Desulfolinea sp018648605	80.0229	411	1180	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__Desulfolinea	95.0	99.90	99.89	0.94	0.91	3	-
GCA_018645405.1	s__Desulfolinea sp018645405	79.115	508	1180	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__Desulfolinea	95.0	99.86	99.73	0.91	0.78	10	-
GCA_016744335.1	s__Desulfolinea sp016744335	78.0359	273	1180	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__Desulfolinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014382535.1	s__Desulfolinea nitratireducens	77.1747	238	1180	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__Desulfolinea	95.0	99.72	99.72	0.90	0.90	2	-
GCA_013152325.1	s__Desulfolinea sp013152325	75.7946	51	1180	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__Desulfolinea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 00:36:42,375] [INFO] GTDB search result was written to OceanDNA-b13566/result_gtdb.tsv
[2023-03-18 00:36:42,375] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:36:42,376] [INFO] DFAST_QC result json was written to OceanDNA-b13566/dqc_result.json
[2023-03-18 00:36:42,376] [INFO] DFAST_QC completed!
[2023-03-18 00:36:42,376] [INFO] Total running time: 0h1m36s