[2023-03-18 00:35:06,598] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:35:06,598] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:35:06,599] [INFO] DQC Reference Directory: /var/lib/cwl/stg79cddef3-708b-46b4-ae04-fc5444b8164f/dqc_reference
[2023-03-18 00:35:07,705] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:35:07,705] [INFO] Task started: Prodigal
[2023-03-18 00:35:07,706] [INFO] Running command: cat /var/lib/cwl/stgf3620bd4-cc25-48d5-9ffc-a61bde6bf31f/OceanDNA-b2219.fa | prodigal -d OceanDNA-b2219/cds.fna -a OceanDNA-b2219/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:35:11,393] [INFO] Task succeeded: Prodigal
[2023-03-18 00:35:11,394] [INFO] Task started: HMMsearch
[2023-03-18 00:35:11,394] [INFO] Running command: hmmsearch --tblout OceanDNA-b2219/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg79cddef3-708b-46b4-ae04-fc5444b8164f/dqc_reference/reference_markers.hmm OceanDNA-b2219/protein.faa > /dev/null
[2023-03-18 00:35:11,559] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:35:11,559] [INFO] Found 6/6 markers.
[2023-03-18 00:35:11,566] [INFO] Query marker FASTA was written to OceanDNA-b2219/markers.fasta
[2023-03-18 00:35:11,566] [INFO] Task started: Blastn
[2023-03-18 00:35:11,566] [INFO] Running command: blastn -query OceanDNA-b2219/markers.fasta -db /var/lib/cwl/stg79cddef3-708b-46b4-ae04-fc5444b8164f/dqc_reference/reference_markers.fasta -out OceanDNA-b2219/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:35:12,090] [INFO] Task succeeded: Blastn
[2023-03-18 00:35:12,091] [INFO] Selected 5 target genomes.
[2023-03-18 00:35:12,091] [INFO] Target genome list was writen to OceanDNA-b2219/target_genomes.txt
[2023-03-18 00:35:12,094] [INFO] Task started: fastANI
[2023-03-18 00:35:12,094] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3620bd4-cc25-48d5-9ffc-a61bde6bf31f/OceanDNA-b2219.fa --refList OceanDNA-b2219/target_genomes.txt --output OceanDNA-b2219/fastani_result.tsv --threads 1
[2023-03-18 00:35:13,663] [INFO] Task succeeded: fastANI
[2023-03-18 00:35:13,663] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg79cddef3-708b-46b4-ae04-fc5444b8164f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:35:13,663] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg79cddef3-708b-46b4-ae04-fc5444b8164f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:35:13,663] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:35:13,663] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 00:35:13,664] [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 00:35:13,664] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2219/tc_result.tsv
[2023-03-18 00:35:13,664] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:35:13,664] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:35:13,664] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg79cddef3-708b-46b4-ae04-fc5444b8164f/dqc_reference/checkm_data
[2023-03-18 00:35:13,679] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:35:13,681] [INFO] Task started: CheckM
[2023-03-18 00:35:13,681] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2219/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2219/checkm_input OceanDNA-b2219/checkm_result
[2023-03-18 00:35:31,090] [INFO] Task succeeded: CheckM
[2023-03-18 00:35:31,091] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 00:35:31,092] [INFO] ===== Completeness check finished =====
[2023-03-18 00:35:31,092] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:35:31,092] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2219/markers.fasta)
[2023-03-18 00:35:31,094] [INFO] Task started: Blastn
[2023-03-18 00:35:31,094] [INFO] Running command: blastn -query OceanDNA-b2219/markers.fasta -db /var/lib/cwl/stg79cddef3-708b-46b4-ae04-fc5444b8164f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2219/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:35:32,050] [INFO] Task succeeded: Blastn
[2023-03-18 00:35:32,051] [INFO] Selected 20 target genomes.
[2023-03-18 00:35:32,051] [INFO] Target genome list was writen to OceanDNA-b2219/target_genomes_gtdb.txt
[2023-03-18 00:35:32,072] [INFO] Task started: fastANI
[2023-03-18 00:35:32,072] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3620bd4-cc25-48d5-9ffc-a61bde6bf31f/OceanDNA-b2219.fa --refList OceanDNA-b2219/target_genomes_gtdb.txt --output OceanDNA-b2219/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:35:36,248] [INFO] Task succeeded: fastANI
[2023-03-18 00:35:36,255] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 00:35:36,255] [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_002169845.1	s__Actinomarina sp002169845	98.5053	143	229	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_014239265.1	s__Actinomarina sp014239265	82.8944	176	229	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902510965.1	s__Actinomarina sp002683085	82.5262	133	229	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	98.49	98.44	0.76	0.76	3	-
GCA_002308095.1	s__Actinomarina sp002308095	81.0573	105	229	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014384285.1	s__Actinomarina sp014384285	80.8885	152	229	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	99.05	98.78	0.90	0.82	4	-
GCA_002169115.2	s__Actinomarina sp002169115	79.5876	65	229	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	96.47	96.47	0.52	0.52	2	-
GCA_902599555.1	s__Actinomarina sp902599555	77.8326	52	229	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902625455.1	s__Actinomarina sp902625455	77.7405	56	229	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	97.46	97.35	0.85	0.81	4	-
GCA_003213165.1	s__Actinomarina sp003213165	77.3961	59	229	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	97.69	95.56	0.85	0.73	10	-
GCA_902627635.1	s__Actinomarina sp902627635	77.2118	54	229	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902565645.1	s__Actinomarina sp902565645	77.0844	54	229	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 00:35:36,255] [INFO] GTDB search result was written to OceanDNA-b2219/result_gtdb.tsv
[2023-03-18 00:35:36,255] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:35:36,256] [INFO] DFAST_QC result json was written to OceanDNA-b2219/dqc_result.json
[2023-03-18 00:35:36,256] [INFO] DFAST_QC completed!
[2023-03-18 00:35:36,257] [INFO] Total running time: 0h0m30s