[2023-03-19 03:50:07,837] [INFO] DFAST_QC pipeline started.
[2023-03-19 03:50:07,837] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 03:50:07,838] [INFO] DQC Reference Directory: /var/lib/cwl/stg2739c3c2-24cf-4b7a-bcff-02a6c8476beb/dqc_reference
[2023-03-19 03:50:09,608] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 03:50:09,609] [INFO] Task started: Prodigal
[2023-03-19 03:50:09,609] [INFO] Running command: cat /var/lib/cwl/stgb7264699-1da9-42b3-8802-b4868230e68f/OceanDNA-b2297.fa | prodigal -d OceanDNA-b2297/cds.fna -a OceanDNA-b2297/protein.faa -g 11 -q > /dev/null
[2023-03-19 03:50:13,918] [INFO] Task succeeded: Prodigal
[2023-03-19 03:50:13,922] [INFO] Task started: HMMsearch
[2023-03-19 03:50:13,922] [INFO] Running command: hmmsearch --tblout OceanDNA-b2297/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2739c3c2-24cf-4b7a-bcff-02a6c8476beb/dqc_reference/reference_markers.hmm OceanDNA-b2297/protein.faa > /dev/null
[2023-03-19 03:50:14,109] [INFO] Task succeeded: HMMsearch
[2023-03-19 03:50:14,110] [INFO] Found 6/6 markers.
[2023-03-19 03:50:14,117] [INFO] Query marker FASTA was written to OceanDNA-b2297/markers.fasta
[2023-03-19 03:50:14,117] [INFO] Task started: Blastn
[2023-03-19 03:50:14,117] [INFO] Running command: blastn -query OceanDNA-b2297/markers.fasta -db /var/lib/cwl/stg2739c3c2-24cf-4b7a-bcff-02a6c8476beb/dqc_reference/reference_markers.fasta -out OceanDNA-b2297/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:50:14,615] [INFO] Task succeeded: Blastn
[2023-03-19 03:50:14,616] [INFO] Selected 9 target genomes.
[2023-03-19 03:50:14,616] [INFO] Target genome list was writen to OceanDNA-b2297/target_genomes.txt
[2023-03-19 03:50:14,621] [INFO] Task started: fastANI
[2023-03-19 03:50:14,621] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7264699-1da9-42b3-8802-b4868230e68f/OceanDNA-b2297.fa --refList OceanDNA-b2297/target_genomes.txt --output OceanDNA-b2297/fastani_result.tsv --threads 1
[2023-03-19 03:50:19,706] [INFO] Task succeeded: fastANI
[2023-03-19 03:50:19,706] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2739c3c2-24cf-4b7a-bcff-02a6c8476beb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 03:50:19,706] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2739c3c2-24cf-4b7a-bcff-02a6c8476beb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 03:50:19,707] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 03:50:19,707] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 03:50:19,707] [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
--------------------------------------------------------------------------------
[2023-03-19 03:50:19,707] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2297/tc_result.tsv
[2023-03-19 03:50:19,707] [INFO] ===== Taxonomy check completed =====
[2023-03-19 03:50:19,707] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 03:50:19,707] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2739c3c2-24cf-4b7a-bcff-02a6c8476beb/dqc_reference/checkm_data
[2023-03-19 03:50:19,710] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 03:50:19,712] [INFO] Task started: CheckM
[2023-03-19 03:50:19,712] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2297/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2297/checkm_input OceanDNA-b2297/checkm_result
[2023-03-19 03:50:36,521] [INFO] Task succeeded: CheckM
[2023-03-19 03:50:36,522] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 03:50:36,523] [INFO] ===== Completeness check finished =====
[2023-03-19 03:50:36,523] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:50:36,524] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2297/markers.fasta)
[2023-03-19 03:50:36,524] [INFO] Task started: Blastn
[2023-03-19 03:50:36,524] [INFO] Running command: blastn -query OceanDNA-b2297/markers.fasta -db /var/lib/cwl/stg2739c3c2-24cf-4b7a-bcff-02a6c8476beb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2297/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:50:37,259] [INFO] Task succeeded: Blastn
[2023-03-19 03:50:37,260] [INFO] Selected 14 target genomes.
[2023-03-19 03:50:37,260] [INFO] Target genome list was writen to OceanDNA-b2297/target_genomes_gtdb.txt
[2023-03-19 03:50:37,278] [INFO] Task started: fastANI
[2023-03-19 03:50:37,279] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7264699-1da9-42b3-8802-b4868230e68f/OceanDNA-b2297.fa --refList OceanDNA-b2297/target_genomes_gtdb.txt --output OceanDNA-b2297/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:50:39,864] [INFO] Task succeeded: fastANI
[2023-03-19 03:50:39,871] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 03:50:39,872] [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_002308095.1	s__Actinomarina sp002308095	98.483	169	271	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014384285.1	s__Actinomarina sp014384285	81.6816	207	271	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	99.05	98.78	0.90	0.82	4	-
GCA_902510965.1	s__Actinomarina sp002683085	80.8949	135	271	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	98.49	98.44	0.76	0.76	3	-
GCA_014239265.1	s__Actinomarina sp014239265	80.4498	160	271	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002169845.1	s__Actinomarina sp002169845	80.1428	103	271	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002169115.2	s__Actinomarina sp002169115	78.8799	63	271	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	96.47	96.47	0.52	0.52	2	-
GCA_902519215.1	s__Actinomarina sp902519215	78.5747	54	271	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	96.27	96.27	0.84	0.84	2	-
GCA_902599555.1	s__Actinomarina sp902599555	78.0845	63	271	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902555985.1	s__Actinomarina sp902555985	78.024	65	271	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	97.40	96.59	0.85	0.83	4	-
GCA_902533795.1	s__Actinomarina sp902533795	77.9924	54	271	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	95.75	95.75	0.81	0.81	2	-
GCA_902510995.1	s__Actinomarina sp902510995	77.981	68	271	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	95.36	95.36	0.76	0.76	2	-
GCA_902626065.1	s__Actinomarina sp902626065	77.1473	64	271	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	96.15	96.15	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2023-03-19 03:50:39,872] [INFO] GTDB search result was written to OceanDNA-b2297/result_gtdb.tsv
[2023-03-19 03:50:39,872] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:50:39,873] [INFO] DFAST_QC result json was written to OceanDNA-b2297/dqc_result.json
[2023-03-19 03:50:39,873] [INFO] DFAST_QC completed!
[2023-03-19 03:50:39,873] [INFO] Total running time: 0h0m32s