[2023-03-16 05:27:23,880] [INFO] DFAST_QC pipeline started.
[2023-03-16 05:27:23,889] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 05:27:23,889] [INFO] DQC Reference Directory: /var/lib/cwl/stg0540d58c-87dd-4f00-beb4-2b4f2761b65c/dqc_reference
[2023-03-16 05:27:24,988] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 05:27:24,988] [INFO] Task started: Prodigal
[2023-03-16 05:27:24,989] [INFO] Running command: cat /var/lib/cwl/stg4286bd7f-74b3-4401-acce-0086aeae2d7b/OceanDNA-b14920.fa | prodigal -d OceanDNA-b14920/cds.fna -a OceanDNA-b14920/protein.faa -g 11 -q > /dev/null
[2023-03-16 05:27:30,479] [INFO] Task succeeded: Prodigal
[2023-03-16 05:27:30,479] [INFO] Task started: HMMsearch
[2023-03-16 05:27:30,479] [INFO] Running command: hmmsearch --tblout OceanDNA-b14920/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0540d58c-87dd-4f00-beb4-2b4f2761b65c/dqc_reference/reference_markers.hmm OceanDNA-b14920/protein.faa > /dev/null
[2023-03-16 05:27:30,657] [INFO] Task succeeded: HMMsearch
[2023-03-16 05:27:30,658] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4286bd7f-74b3-4401-acce-0086aeae2d7b/OceanDNA-b14920.fa]
[2023-03-16 05:27:30,772] [INFO] Query marker FASTA was written to OceanDNA-b14920/markers.fasta
[2023-03-16 05:27:30,772] [INFO] Task started: Blastn
[2023-03-16 05:27:30,772] [INFO] Running command: blastn -query OceanDNA-b14920/markers.fasta -db /var/lib/cwl/stg0540d58c-87dd-4f00-beb4-2b4f2761b65c/dqc_reference/reference_markers.fasta -out OceanDNA-b14920/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:27:31,296] [INFO] Task succeeded: Blastn
[2023-03-16 05:27:31,334] [INFO] Selected 17 target genomes.
[2023-03-16 05:27:31,334] [INFO] Target genome list was writen to OceanDNA-b14920/target_genomes.txt
[2023-03-16 05:27:31,343] [INFO] Task started: fastANI
[2023-03-16 05:27:31,343] [INFO] Running command: fastANI --query /var/lib/cwl/stg4286bd7f-74b3-4401-acce-0086aeae2d7b/OceanDNA-b14920.fa --refList OceanDNA-b14920/target_genomes.txt --output OceanDNA-b14920/fastani_result.tsv --threads 1
[2023-03-16 05:27:40,373] [INFO] Task succeeded: fastANI
[2023-03-16 05:27:40,373] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0540d58c-87dd-4f00-beb4-2b4f2761b65c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 05:27:40,374] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0540d58c-87dd-4f00-beb4-2b4f2761b65c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 05:27:40,374] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 05:27:40,374] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 05:27:40,374] [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
--------------------------------------------------------------------------------
[2023-03-16 05:27:40,376] [INFO] DFAST Taxonomy check result was written to OceanDNA-b14920/tc_result.tsv
[2023-03-16 05:27:40,379] [INFO] ===== Taxonomy check completed =====
[2023-03-16 05:27:40,379] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 05:27:40,379] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0540d58c-87dd-4f00-beb4-2b4f2761b65c/dqc_reference/checkm_data
[2023-03-16 05:27:40,382] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 05:27:40,403] [INFO] Task started: CheckM
[2023-03-16 05:27:40,403] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b14920/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b14920/checkm_input OceanDNA-b14920/checkm_result
[2023-03-16 05:27:59,903] [INFO] Task succeeded: CheckM
[2023-03-16 05:27:59,903] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 05:28:00,044] [INFO] ===== Completeness check finished =====
[2023-03-16 05:28:00,044] [INFO] ===== Start GTDB Search =====
[2023-03-16 05:28:00,044] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b14920/markers.fasta)
[2023-03-16 05:28:00,045] [INFO] Task started: Blastn
[2023-03-16 05:28:00,045] [INFO] Running command: blastn -query OceanDNA-b14920/markers.fasta -db /var/lib/cwl/stg0540d58c-87dd-4f00-beb4-2b4f2761b65c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b14920/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:28:00,753] [INFO] Task succeeded: Blastn
[2023-03-16 05:28:00,754] [INFO] Selected 9 target genomes.
[2023-03-16 05:28:00,754] [INFO] Target genome list was writen to OceanDNA-b14920/target_genomes_gtdb.txt
[2023-03-16 05:28:00,764] [INFO] Task started: fastANI
[2023-03-16 05:28:00,764] [INFO] Running command: fastANI --query /var/lib/cwl/stg4286bd7f-74b3-4401-acce-0086aeae2d7b/OceanDNA-b14920.fa --refList OceanDNA-b14920/target_genomes_gtdb.txt --output OceanDNA-b14920/fastani_result_gtdb.tsv --threads 1
[2023-03-16 05:28:03,123] [INFO] Task succeeded: fastANI
[2023-03-16 05:28:03,128] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 05:28:03,128] [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_002171675.1	s__TMED-70 sp002171675	98.6026	318	364	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__TMED-70;g__TMED-70	95.0	99.24	99.20	0.89	0.87	3	conclusive
GCA_008373205.1	s__TMED-70 sp008373205	94.1041	325	364	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__TMED-70;g__TMED-70	95.0	99.62	99.62	0.87	0.87	2	-
GCA_002721875.1	s__TMED-70 sp002721875	82.1413	230	364	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__TMED-70;g__TMED-70	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937255.1	s__TMED-70 sp009937255	78.1332	177	364	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__TMED-70;g__TMED-70	95.0	96.35	96.35	0.92	0.92	2	-
GCA_002703265.1	s__TMED-70 sp002703265	77.8801	152	364	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__TMED-70;g__TMED-70	95.0	97.70	96.59	0.89	0.70	8	-
GCA_002710135.1	s__TMED-70 sp002710135	77.351	107	364	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__TMED-70;g__TMED-70	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002718455.1	s__GCA-2718455 sp002718455	76.7148	76	364	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__TMED-70;g__GCA-2718455	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 05:28:03,128] [INFO] GTDB search result was written to OceanDNA-b14920/result_gtdb.tsv
[2023-03-16 05:28:03,128] [INFO] ===== GTDB Search completed =====
[2023-03-16 05:28:03,129] [INFO] DFAST_QC result json was written to OceanDNA-b14920/dqc_result.json
[2023-03-16 05:28:03,129] [INFO] DFAST_QC completed!
[2023-03-16 05:28:03,129] [INFO] Total running time: 0h0m39s