[2023-03-17 16:13:55,289] [INFO] DFAST_QC pipeline started.
[2023-03-17 16:13:55,290] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 16:13:55,290] [INFO] DQC Reference Directory: /var/lib/cwl/stg3f1db456-b07e-48f4-abe4-9f5611bc4a0e/dqc_reference
[2023-03-17 16:13:56,398] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 16:13:56,399] [INFO] Task started: Prodigal
[2023-03-17 16:13:56,399] [INFO] Running command: cat /var/lib/cwl/stgf2013ed0-f0c5-423e-b28b-a1d6db2ba7db/OceanDNA-b2191.fa | prodigal -d OceanDNA-b2191/cds.fna -a OceanDNA-b2191/protein.faa -g 11 -q > /dev/null
[2023-03-17 16:14:00,990] [INFO] Task succeeded: Prodigal
[2023-03-17 16:14:00,990] [INFO] Task started: HMMsearch
[2023-03-17 16:14:00,990] [INFO] Running command: hmmsearch --tblout OceanDNA-b2191/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3f1db456-b07e-48f4-abe4-9f5611bc4a0e/dqc_reference/reference_markers.hmm OceanDNA-b2191/protein.faa > /dev/null
[2023-03-17 16:14:01,153] [INFO] Task succeeded: HMMsearch
[2023-03-17 16:14:01,153] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf2013ed0-f0c5-423e-b28b-a1d6db2ba7db/OceanDNA-b2191.fa]
[2023-03-17 16:14:01,162] [INFO] Query marker FASTA was written to OceanDNA-b2191/markers.fasta
[2023-03-17 16:14:01,164] [INFO] Task started: Blastn
[2023-03-17 16:14:01,164] [INFO] Running command: blastn -query OceanDNA-b2191/markers.fasta -db /var/lib/cwl/stg3f1db456-b07e-48f4-abe4-9f5611bc4a0e/dqc_reference/reference_markers.fasta -out OceanDNA-b2191/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 16:14:01,832] [INFO] Task succeeded: Blastn
[2023-03-17 16:14:01,832] [INFO] Selected 14 target genomes.
[2023-03-17 16:14:01,832] [INFO] Target genome list was writen to OceanDNA-b2191/target_genomes.txt
[2023-03-17 16:14:01,842] [INFO] Task started: fastANI
[2023-03-17 16:14:01,842] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2013ed0-f0c5-423e-b28b-a1d6db2ba7db/OceanDNA-b2191.fa --refList OceanDNA-b2191/target_genomes.txt --output OceanDNA-b2191/fastani_result.tsv --threads 1
[2023-03-17 16:14:07,860] [INFO] Task succeeded: fastANI
[2023-03-17 16:14:07,860] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3f1db456-b07e-48f4-abe4-9f5611bc4a0e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 16:14:07,860] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3f1db456-b07e-48f4-abe4-9f5611bc4a0e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 16:14:07,860] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 16:14:07,860] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 16:14:07,860] [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 16:14:07,861] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2191/tc_result.tsv
[2023-03-17 16:14:07,861] [INFO] ===== Taxonomy check completed =====
[2023-03-17 16:14:07,861] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 16:14:07,861] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3f1db456-b07e-48f4-abe4-9f5611bc4a0e/dqc_reference/checkm_data
[2023-03-17 16:14:07,863] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 16:14:07,866] [INFO] Task started: CheckM
[2023-03-17 16:14:07,866] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2191/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2191/checkm_input OceanDNA-b2191/checkm_result
[2023-03-17 16:14:30,811] [INFO] Task succeeded: CheckM
[2023-03-17 16:14:30,812] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 16:14:30,813] [INFO] ===== Completeness check finished =====
[2023-03-17 16:14:30,813] [INFO] ===== Start GTDB Search =====
[2023-03-17 16:14:30,813] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2191/markers.fasta)
[2023-03-17 16:14:30,815] [INFO] Task started: Blastn
[2023-03-17 16:14:30,815] [INFO] Running command: blastn -query OceanDNA-b2191/markers.fasta -db /var/lib/cwl/stg3f1db456-b07e-48f4-abe4-9f5611bc4a0e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2191/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 16:14:32,368] [INFO] Task succeeded: Blastn
[2023-03-17 16:14:32,369] [INFO] Selected 15 target genomes.
[2023-03-17 16:14:32,369] [INFO] Target genome list was writen to OceanDNA-b2191/target_genomes_gtdb.txt
[2023-03-17 16:14:32,744] [INFO] Task started: fastANI
[2023-03-17 16:14:32,744] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2013ed0-f0c5-423e-b28b-a1d6db2ba7db/OceanDNA-b2191.fa --refList OceanDNA-b2191/target_genomes_gtdb.txt --output OceanDNA-b2191/fastani_result_gtdb.tsv --threads 1
[2023-03-17 16:14:40,572] [INFO] Task succeeded: fastANI
[2023-03-17 16:14:40,579] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 16:14:40,579] [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_902555985.1	s__Actinomarina sp902555985	96.2907	271	297	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	97.40	96.59	0.85	0.83	4	conclusive
GCA_902593795.1	s__Actinomarina sp902593795	90.0346	251	297	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	97.69	97.47	0.86	0.85	3	-
GCA_902610815.1	s__Actinomarina sp902610815	81.6275	208	297	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004213405.1	s__Actinomarina sp004213405	81.5299	136	297	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902622665.1	s__Actinomarina sp902622665	81.3094	185	297	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902593475.1	s__Actinomarina sp902593475	81.2674	160	297	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902580215.1	s__Actinomarina sp902580215	81.1475	197	297	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	95.48	95.05	0.79	0.77	5	-
GCA_902628045.1	s__Actinomarina sp902628045	80.9023	185	297	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016777845.1	s__Actinomarina sp016777845	80.8953	149	297	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003281085.1	s__Actinomarina sp003281085	79.3984	109	297	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	96.17	95.08	0.82	0.73	10	-
GCA_902596545.1	s__Actinomarina sp902596545	79.1361	127	297	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	98.42	98.42	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-03-17 16:14:40,579] [INFO] GTDB search result was written to OceanDNA-b2191/result_gtdb.tsv
[2023-03-17 16:14:40,579] [INFO] ===== GTDB Search completed =====
[2023-03-17 16:14:40,580] [INFO] DFAST_QC result json was written to OceanDNA-b2191/dqc_result.json
[2023-03-17 16:14:40,581] [INFO] DFAST_QC completed!
[2023-03-17 16:14:40,581] [INFO] Total running time: 0h0m45s