[2023-03-18 08:41:54,063] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:41:54,063] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:41:54,064] [INFO] DQC Reference Directory: /var/lib/cwl/stg8e3e69ca-bc29-4243-90f5-62591e4442dc/dqc_reference
[2023-03-18 08:41:56,195] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:41:56,196] [INFO] Task started: Prodigal
[2023-03-18 08:41:56,196] [INFO] Running command: cat /var/lib/cwl/stg3e006d08-1051-4ed1-84da-65ba60ee4eef/OceanDNA-b22185.fa | prodigal -d OceanDNA-b22185/cds.fna -a OceanDNA-b22185/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:42:05,391] [INFO] Task succeeded: Prodigal
[2023-03-18 08:42:05,391] [INFO] Task started: HMMsearch
[2023-03-18 08:42:05,391] [INFO] Running command: hmmsearch --tblout OceanDNA-b22185/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8e3e69ca-bc29-4243-90f5-62591e4442dc/dqc_reference/reference_markers.hmm OceanDNA-b22185/protein.faa > /dev/null
[2023-03-18 08:42:05,602] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:42:05,603] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg3e006d08-1051-4ed1-84da-65ba60ee4eef/OceanDNA-b22185.fa]
[2023-03-18 08:42:05,619] [INFO] Query marker FASTA was written to OceanDNA-b22185/markers.fasta
[2023-03-18 08:42:05,621] [INFO] Task started: Blastn
[2023-03-18 08:42:05,621] [INFO] Running command: blastn -query OceanDNA-b22185/markers.fasta -db /var/lib/cwl/stg8e3e69ca-bc29-4243-90f5-62591e4442dc/dqc_reference/reference_markers.fasta -out OceanDNA-b22185/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:42:08,539] [INFO] Task succeeded: Blastn
[2023-03-18 08:42:08,540] [INFO] Selected 16 target genomes.
[2023-03-18 08:42:08,540] [INFO] Target genome list was writen to OceanDNA-b22185/target_genomes.txt
[2023-03-18 08:42:08,549] [INFO] Task started: fastANI
[2023-03-18 08:42:08,549] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e006d08-1051-4ed1-84da-65ba60ee4eef/OceanDNA-b22185.fa --refList OceanDNA-b22185/target_genomes.txt --output OceanDNA-b22185/fastani_result.tsv --threads 1
[2023-03-18 08:42:19,650] [INFO] Task succeeded: fastANI
[2023-03-18 08:42:19,650] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8e3e69ca-bc29-4243-90f5-62591e4442dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:42:19,650] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8e3e69ca-bc29-4243-90f5-62591e4442dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:42:19,650] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:42:19,650] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 08:42:19,650] [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 08:42:19,651] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22185/tc_result.tsv
[2023-03-18 08:42:19,651] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:42:19,651] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:42:19,651] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8e3e69ca-bc29-4243-90f5-62591e4442dc/dqc_reference/checkm_data
[2023-03-18 08:42:19,707] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:42:20,016] [INFO] Task started: CheckM
[2023-03-18 08:42:20,016] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22185/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22185/checkm_input OceanDNA-b22185/checkm_result
[2023-03-18 08:42:51,703] [INFO] Task succeeded: CheckM
[2023-03-18 08:42:51,703] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.31%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:42:51,705] [INFO] ===== Completeness check finished =====
[2023-03-18 08:42:51,706] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:42:51,706] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22185/markers.fasta)
[2023-03-18 08:42:51,708] [INFO] Task started: Blastn
[2023-03-18 08:42:51,708] [INFO] Running command: blastn -query OceanDNA-b22185/markers.fasta -db /var/lib/cwl/stg8e3e69ca-bc29-4243-90f5-62591e4442dc/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22185/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:42:52,363] [INFO] Task succeeded: Blastn
[2023-03-18 08:42:52,363] [INFO] Selected 13 target genomes.
[2023-03-18 08:42:52,364] [INFO] Target genome list was writen to OceanDNA-b22185/target_genomes_gtdb.txt
[2023-03-18 08:42:52,371] [INFO] Task started: fastANI
[2023-03-18 08:42:52,372] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e006d08-1051-4ed1-84da-65ba60ee4eef/OceanDNA-b22185.fa --refList OceanDNA-b22185/target_genomes_gtdb.txt --output OceanDNA-b22185/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:42:58,913] [INFO] Task succeeded: fastANI
[2023-03-18 08:42:58,919] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 08:42:58,919] [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_002709295.1	s__GCA-002862325 sp002709295	99.6625	370	376	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002862325	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002683195.1	s__GCA-002862325 sp002683195	78.3063	145	376	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002862325	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002684755.1	s__UBA12014 sp002684755	78.1642	116	376	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA12014	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862325.1	s__GCA-002862325 sp002862325	78.0437	91	376	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002862325	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009936695.1	s__UBA12014 sp009936695	77.8273	102	376	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA12014	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002685335.1	s__GCA-002862325 sp002685335	77.8126	80	376	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002862325	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002683215.1	s__UBA12014 sp002683215	77.6679	106	376	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA12014	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002167845.2	s__UBA12014 sp002167845	77.1206	96	376	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA12014	95.0	99.48	99.48	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-03-18 08:42:58,920] [INFO] GTDB search result was written to OceanDNA-b22185/result_gtdb.tsv
[2023-03-18 08:42:58,920] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:42:58,921] [INFO] DFAST_QC result json was written to OceanDNA-b22185/dqc_result.json
[2023-03-18 08:42:58,921] [INFO] DFAST_QC completed!
[2023-03-18 08:42:58,921] [INFO] Total running time: 0h1m5s