[2023-03-16 07:13:34,675] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:13:34,675] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:13:34,675] [INFO] DQC Reference Directory: /var/lib/cwl/stgcf71138b-8ee4-4506-8861-a024b0a11dbe/dqc_reference
[2023-03-16 07:13:35,801] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:13:35,801] [INFO] Task started: Prodigal
[2023-03-16 07:13:35,801] [INFO] Running command: cat /var/lib/cwl/stgdd0aea37-c7bc-407a-98f7-efa278001cb2/OceanDNA-b46349.fa | prodigal -d OceanDNA-b46349/cds.fna -a OceanDNA-b46349/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:14:10,647] [INFO] Task succeeded: Prodigal
[2023-03-16 07:14:10,647] [INFO] Task started: HMMsearch
[2023-03-16 07:14:10,647] [INFO] Running command: hmmsearch --tblout OceanDNA-b46349/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcf71138b-8ee4-4506-8861-a024b0a11dbe/dqc_reference/reference_markers.hmm OceanDNA-b46349/protein.faa > /dev/null
[2023-03-16 07:14:10,834] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:14:10,835] [INFO] Found 6/6 markers.
[2023-03-16 07:14:10,859] [INFO] Query marker FASTA was written to OceanDNA-b46349/markers.fasta
[2023-03-16 07:14:10,860] [INFO] Task started: Blastn
[2023-03-16 07:14:10,860] [INFO] Running command: blastn -query OceanDNA-b46349/markers.fasta -db /var/lib/cwl/stgcf71138b-8ee4-4506-8861-a024b0a11dbe/dqc_reference/reference_markers.fasta -out OceanDNA-b46349/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:14:11,412] [INFO] Task succeeded: Blastn
[2023-03-16 07:14:11,413] [INFO] Selected 25 target genomes.
[2023-03-16 07:14:11,413] [INFO] Target genome list was writen to OceanDNA-b46349/target_genomes.txt
[2023-03-16 07:14:11,428] [INFO] Task started: fastANI
[2023-03-16 07:14:11,428] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd0aea37-c7bc-407a-98f7-efa278001cb2/OceanDNA-b46349.fa --refList OceanDNA-b46349/target_genomes.txt --output OceanDNA-b46349/fastani_result.tsv --threads 1
[2023-03-16 07:14:28,394] [INFO] Task succeeded: fastANI
[2023-03-16 07:14:28,394] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcf71138b-8ee4-4506-8861-a024b0a11dbe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:14:28,395] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcf71138b-8ee4-4506-8861-a024b0a11dbe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:14:28,398] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 07:14:28,398] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 07:14:28,398] [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
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	75.1218	51	1211	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 07:14:28,398] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46349/tc_result.tsv
[2023-03-16 07:14:28,398] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:14:28,399] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:14:28,399] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcf71138b-8ee4-4506-8861-a024b0a11dbe/dqc_reference/checkm_data
[2023-03-16 07:14:28,399] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:14:28,405] [INFO] Task started: CheckM
[2023-03-16 07:14:28,405] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46349/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46349/checkm_input OceanDNA-b46349/checkm_result
[2023-03-16 07:15:53,356] [INFO] Task succeeded: CheckM
[2023-03-16 07:15:53,356] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 07:15:53,359] [INFO] ===== Completeness check finished =====
[2023-03-16 07:15:53,359] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:15:53,359] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46349/markers.fasta)
[2023-03-16 07:15:53,361] [INFO] Task started: Blastn
[2023-03-16 07:15:53,361] [INFO] Running command: blastn -query OceanDNA-b46349/markers.fasta -db /var/lib/cwl/stgcf71138b-8ee4-4506-8861-a024b0a11dbe/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46349/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:15:54,189] [INFO] Task succeeded: Blastn
[2023-03-16 07:15:54,190] [INFO] Selected 8 target genomes.
[2023-03-16 07:15:54,190] [INFO] Target genome list was writen to OceanDNA-b46349/target_genomes_gtdb.txt
[2023-03-16 07:15:54,198] [INFO] Task started: fastANI
[2023-03-16 07:15:54,198] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd0aea37-c7bc-407a-98f7-efa278001cb2/OceanDNA-b46349.fa --refList OceanDNA-b46349/target_genomes_gtdb.txt --output OceanDNA-b46349/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:16:00,012] [INFO] Task succeeded: fastANI
[2023-03-16 07:16:00,017] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 07:16:00,017] [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_015658765.1	s__UBA1096 sp015658765	95.9993	489	1211	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018674955.1	s__UBA1096 sp018674955	91.8352	827	1211	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	98.88	98.74	0.86	0.81	14	-
GCA_002299785.1	s__UBA1096 sp002299785	90.7254	565	1211	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003972865.1	s__UBA1096 sp003972865	88.8941	616	1211	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014382705.1	s__UBA1096 sp014382705	85.0074	846	1211	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002686755.1	s__UBA1096 sp002686755	83.2929	736	1211	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002453165.1	s__UBA1096 sp002453165	78.9512	443	1211	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1096;g__UBA1096	95.0	96.70	95.18	0.81	0.76	7	-
--------------------------------------------------------------------------------
[2023-03-16 07:16:00,018] [INFO] GTDB search result was written to OceanDNA-b46349/result_gtdb.tsv
[2023-03-16 07:16:00,018] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:16:00,019] [INFO] DFAST_QC result json was written to OceanDNA-b46349/dqc_result.json
[2023-03-16 07:16:00,019] [INFO] DFAST_QC completed!
[2023-03-16 07:16:00,019] [INFO] Total running time: 0h2m25s