[2023-03-17 10:08:39,145] [INFO] DFAST_QC pipeline started.
[2023-03-17 10:08:39,145] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 10:08:39,146] [INFO] DQC Reference Directory: /var/lib/cwl/stga4158939-1533-4526-bc6b-75d91094dcef/dqc_reference
[2023-03-17 10:08:40,269] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 10:08:40,269] [INFO] Task started: Prodigal
[2023-03-17 10:08:40,270] [INFO] Running command: cat /var/lib/cwl/stg57331a9f-d861-4464-890e-102d4c8c8f2d/OceanDNA-b18094.fa | prodigal -d OceanDNA-b18094/cds.fna -a OceanDNA-b18094/protein.faa -g 11 -q > /dev/null
[2023-03-17 10:08:44,415] [INFO] Task succeeded: Prodigal
[2023-03-17 10:08:44,416] [INFO] Task started: HMMsearch
[2023-03-17 10:08:44,416] [INFO] Running command: hmmsearch --tblout OceanDNA-b18094/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga4158939-1533-4526-bc6b-75d91094dcef/dqc_reference/reference_markers.hmm OceanDNA-b18094/protein.faa > /dev/null
[2023-03-17 10:08:44,563] [INFO] Task succeeded: HMMsearch
[2023-03-17 10:08:44,564] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg57331a9f-d861-4464-890e-102d4c8c8f2d/OceanDNA-b18094.fa]
[2023-03-17 10:08:44,570] [INFO] Query marker FASTA was written to OceanDNA-b18094/markers.fasta
[2023-03-17 10:08:44,570] [INFO] Task started: Blastn
[2023-03-17 10:08:44,571] [INFO] Running command: blastn -query OceanDNA-b18094/markers.fasta -db /var/lib/cwl/stga4158939-1533-4526-bc6b-75d91094dcef/dqc_reference/reference_markers.fasta -out OceanDNA-b18094/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:08:45,127] [INFO] Task succeeded: Blastn
[2023-03-17 10:08:45,127] [INFO] Selected 17 target genomes.
[2023-03-17 10:08:45,128] [INFO] Target genome list was writen to OceanDNA-b18094/target_genomes.txt
[2023-03-17 10:08:45,137] [INFO] Task started: fastANI
[2023-03-17 10:08:45,137] [INFO] Running command: fastANI --query /var/lib/cwl/stg57331a9f-d861-4464-890e-102d4c8c8f2d/OceanDNA-b18094.fa --refList OceanDNA-b18094/target_genomes.txt --output OceanDNA-b18094/fastani_result.tsv --threads 1
[2023-03-17 10:08:52,709] [INFO] Task succeeded: fastANI
[2023-03-17 10:08:52,709] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga4158939-1533-4526-bc6b-75d91094dcef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 10:08:52,710] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga4158939-1533-4526-bc6b-75d91094dcef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 10:08:52,710] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 10:08:52,710] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 10:08:52,710] [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 10:08:52,710] [INFO] DFAST Taxonomy check result was written to OceanDNA-b18094/tc_result.tsv
[2023-03-17 10:08:52,710] [INFO] ===== Taxonomy check completed =====
[2023-03-17 10:08:52,710] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 10:08:52,711] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga4158939-1533-4526-bc6b-75d91094dcef/dqc_reference/checkm_data
[2023-03-17 10:08:52,714] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 10:08:52,716] [INFO] Task started: CheckM
[2023-03-17 10:08:52,716] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b18094/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b18094/checkm_input OceanDNA-b18094/checkm_result
[2023-03-17 10:09:09,639] [INFO] Task succeeded: CheckM
[2023-03-17 10:09:09,639] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 10:09:09,640] [INFO] ===== Completeness check finished =====
[2023-03-17 10:09:09,641] [INFO] ===== Start GTDB Search =====
[2023-03-17 10:09:09,641] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b18094/markers.fasta)
[2023-03-17 10:09:09,642] [INFO] Task started: Blastn
[2023-03-17 10:09:09,642] [INFO] Running command: blastn -query OceanDNA-b18094/markers.fasta -db /var/lib/cwl/stga4158939-1533-4526-bc6b-75d91094dcef/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b18094/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:09:10,280] [INFO] Task succeeded: Blastn
[2023-03-17 10:09:10,281] [INFO] Selected 7 target genomes.
[2023-03-17 10:09:10,281] [INFO] Target genome list was writen to OceanDNA-b18094/target_genomes_gtdb.txt
[2023-03-17 10:09:10,285] [INFO] Task started: fastANI
[2023-03-17 10:09:10,285] [INFO] Running command: fastANI --query /var/lib/cwl/stg57331a9f-d861-4464-890e-102d4c8c8f2d/OceanDNA-b18094.fa --refList OceanDNA-b18094/target_genomes_gtdb.txt --output OceanDNA-b18094/fastani_result_gtdb.tsv --threads 1
[2023-03-17 10:09:11,682] [INFO] Task succeeded: fastANI
[2023-03-17 10:09:11,687] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 10:09:11,687] [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_905182795.1	s__Marinisoma sp905182795	99.8045	261	271	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000402755.1	s__Marinisoma sp000402755	89.8734	225	271	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	95.42	95.16	0.79	0.76	17	-
GCA_002701645.1	s__Marinisoma sp002701645	87.5817	183	271	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014240005.1	s__Marinisoma sp014240005	86.7903	207	271	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	96.63	96.63	0.87	0.87	2	-
GCA_000402815.1	s__Marinisoma atlanticum	84.1562	236	271	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	99.54	99.22	0.95	0.89	4	-
GCA_000402655.1	s__Marinisoma sp000402655	77.8793	85	271	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	96.42	95.83	0.93	0.92	4	-
GCA_902578385.1	s__Marinisoma sp002710515	77.4798	86	271	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	97.88	96.56	0.86	0.83	7	-
--------------------------------------------------------------------------------
[2023-03-17 10:09:11,687] [INFO] GTDB search result was written to OceanDNA-b18094/result_gtdb.tsv
[2023-03-17 10:09:11,687] [INFO] ===== GTDB Search completed =====
[2023-03-17 10:09:11,688] [INFO] DFAST_QC result json was written to OceanDNA-b18094/dqc_result.json
[2023-03-17 10:09:11,688] [INFO] DFAST_QC completed!
[2023-03-17 10:09:11,688] [INFO] Total running time: 0h0m33s