[2023-03-18 07:29:32,041] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:29:32,041] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:29:32,041] [INFO] DQC Reference Directory: /var/lib/cwl/stg9c721c94-5942-473a-933c-be3bb9f3219a/dqc_reference
[2023-03-18 07:29:33,112] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:29:33,112] [INFO] Task started: Prodigal
[2023-03-18 07:29:33,113] [INFO] Running command: cat /var/lib/cwl/stg9a8f92e3-3e43-48b5-ba2e-ee5919dd949a/OceanDNA-b2187.fa | prodigal -d OceanDNA-b2187/cds.fna -a OceanDNA-b2187/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:29:35,713] [INFO] Task succeeded: Prodigal
[2023-03-18 07:29:35,714] [INFO] Task started: HMMsearch
[2023-03-18 07:29:35,714] [INFO] Running command: hmmsearch --tblout OceanDNA-b2187/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9c721c94-5942-473a-933c-be3bb9f3219a/dqc_reference/reference_markers.hmm OceanDNA-b2187/protein.faa > /dev/null
[2023-03-18 07:29:35,848] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:29:35,849] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg9a8f92e3-3e43-48b5-ba2e-ee5919dd949a/OceanDNA-b2187.fa]
[2023-03-18 07:29:35,854] [INFO] Query marker FASTA was written to OceanDNA-b2187/markers.fasta
[2023-03-18 07:29:35,854] [INFO] Task started: Blastn
[2023-03-18 07:29:35,854] [INFO] Running command: blastn -query OceanDNA-b2187/markers.fasta -db /var/lib/cwl/stg9c721c94-5942-473a-933c-be3bb9f3219a/dqc_reference/reference_markers.fasta -out OceanDNA-b2187/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:29:37,653] [INFO] Task succeeded: Blastn
[2023-03-18 07:29:37,654] [INFO] Selected 6 target genomes.
[2023-03-18 07:29:37,654] [INFO] Target genome list was writen to OceanDNA-b2187/target_genomes.txt
[2023-03-18 07:29:37,659] [INFO] Task started: fastANI
[2023-03-18 07:29:37,659] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a8f92e3-3e43-48b5-ba2e-ee5919dd949a/OceanDNA-b2187.fa --refList OceanDNA-b2187/target_genomes.txt --output OceanDNA-b2187/fastani_result.tsv --threads 1
[2023-03-18 07:29:39,529] [INFO] Task succeeded: fastANI
[2023-03-18 07:29:39,530] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9c721c94-5942-473a-933c-be3bb9f3219a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:29:39,530] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9c721c94-5942-473a-933c-be3bb9f3219a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:29:39,530] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:29:39,530] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 07:29:39,530] [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 07:29:39,531] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2187/tc_result.tsv
[2023-03-18 07:29:39,531] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:29:39,531] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:29:39,531] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9c721c94-5942-473a-933c-be3bb9f3219a/dqc_reference/checkm_data
[2023-03-18 07:29:39,541] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:29:39,543] [INFO] Task started: CheckM
[2023-03-18 07:29:39,543] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2187/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2187/checkm_input OceanDNA-b2187/checkm_result
[2023-03-18 07:29:54,968] [INFO] Task succeeded: CheckM
[2023-03-18 07:29:54,969] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 07:29:54,970] [INFO] ===== Completeness check finished =====
[2023-03-18 07:29:54,970] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:29:54,970] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2187/markers.fasta)
[2023-03-18 07:29:54,972] [INFO] Task started: Blastn
[2023-03-18 07:29:54,972] [INFO] Running command: blastn -query OceanDNA-b2187/markers.fasta -db /var/lib/cwl/stg9c721c94-5942-473a-933c-be3bb9f3219a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2187/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:29:55,775] [INFO] Task succeeded: Blastn
[2023-03-18 07:29:55,776] [INFO] Selected 12 target genomes.
[2023-03-18 07:29:55,776] [INFO] Target genome list was writen to OceanDNA-b2187/target_genomes_gtdb.txt
[2023-03-18 07:29:56,003] [INFO] Task started: fastANI
[2023-03-18 07:29:56,003] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a8f92e3-3e43-48b5-ba2e-ee5919dd949a/OceanDNA-b2187.fa --refList OceanDNA-b2187/target_genomes_gtdb.txt --output OceanDNA-b2187/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:29:58,019] [INFO] Task succeeded: fastANI
[2023-03-18 07:29:58,026] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 07:29:58,026] [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_902593795.1	s__Actinomarina sp902593795	98.6891	151	166	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	97.69	97.47	0.86	0.85	3	conclusive
GCA_902555985.1	s__Actinomarina sp902555985	91.4072	149	166	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	97.40	96.59	0.85	0.83	4	-
GCA_902610815.1	s__Actinomarina sp902610815	81.1426	132	166	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	81.0477	88	166	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	80.7888	104	166	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	80.6896	117	166	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	95.48	95.05	0.79	0.77	5	-
GCA_016777845.1	s__Actinomarina sp016777845	80.6223	92	166	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902595195.1	s__Actinomarina sp902595195	79.2265	71	166	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	97.26	97.26	0.73	0.73	2	-
GCA_003281085.1	s__Actinomarina sp003281085	78.964	72	166	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	78.9298	90	166	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	98.42	98.42	0.93	0.93	2	-
GCA_902625455.1	s__Actinomarina sp902625455	78.8378	80	166	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	97.46	97.35	0.85	0.81	4	-
--------------------------------------------------------------------------------
[2023-03-18 07:29:58,026] [INFO] GTDB search result was written to OceanDNA-b2187/result_gtdb.tsv
[2023-03-18 07:29:58,027] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:29:58,027] [INFO] DFAST_QC result json was written to OceanDNA-b2187/dqc_result.json
[2023-03-18 07:29:58,028] [INFO] DFAST_QC completed!
[2023-03-18 07:29:58,028] [INFO] Total running time: 0h0m26s