[2023-03-19 00:29:45,987] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:29:45,987] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:29:45,987] [INFO] DQC Reference Directory: /var/lib/cwl/stg9c71fd04-392f-4721-9876-c81435ce3e62/dqc_reference
[2023-03-19 00:29:47,074] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:29:47,074] [INFO] Task started: Prodigal
[2023-03-19 00:29:47,074] [INFO] Running command: cat /var/lib/cwl/stg0ad3324e-0132-49c8-8aa0-f4d4d59e7c95/OceanDNA-b11149.fa | prodigal -d OceanDNA-b11149/cds.fna -a OceanDNA-b11149/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:29:56,441] [INFO] Task succeeded: Prodigal
[2023-03-19 00:29:56,441] [INFO] Task started: HMMsearch
[2023-03-19 00:29:56,441] [INFO] Running command: hmmsearch --tblout OceanDNA-b11149/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9c71fd04-392f-4721-9876-c81435ce3e62/dqc_reference/reference_markers.hmm OceanDNA-b11149/protein.faa > /dev/null
[2023-03-19 00:29:56,599] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:29:56,600] [INFO] Found 6/6 markers.
[2023-03-19 00:29:56,609] [INFO] Query marker FASTA was written to OceanDNA-b11149/markers.fasta
[2023-03-19 00:29:56,610] [INFO] Task started: Blastn
[2023-03-19 00:29:56,611] [INFO] Running command: blastn -query OceanDNA-b11149/markers.fasta -db /var/lib/cwl/stg9c71fd04-392f-4721-9876-c81435ce3e62/dqc_reference/reference_markers.fasta -out OceanDNA-b11149/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:29:57,144] [INFO] Task succeeded: Blastn
[2023-03-19 00:29:57,145] [INFO] Selected 31 target genomes.
[2023-03-19 00:29:57,145] [INFO] Target genome list was writen to OceanDNA-b11149/target_genomes.txt
[2023-03-19 00:29:57,162] [INFO] Task started: fastANI
[2023-03-19 00:29:57,162] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ad3324e-0132-49c8-8aa0-f4d4d59e7c95/OceanDNA-b11149.fa --refList OceanDNA-b11149/target_genomes.txt --output OceanDNA-b11149/fastani_result.tsv --threads 1
[2023-03-19 00:30:13,505] [INFO] Task succeeded: fastANI
[2023-03-19 00:30:13,505] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9c71fd04-392f-4721-9876-c81435ce3e62/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:30:13,506] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9c71fd04-392f-4721-9876-c81435ce3e62/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:30:13,506] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:30:13,506] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 00:30:13,506] [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
--------------------------------------------------------------------------------
[2023-03-19 00:30:13,506] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11149/tc_result.tsv
[2023-03-19 00:30:13,506] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:30:13,506] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:30:13,506] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9c71fd04-392f-4721-9876-c81435ce3e62/dqc_reference/checkm_data
[2023-03-19 00:30:13,509] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:30:13,513] [INFO] Task started: CheckM
[2023-03-19 00:30:13,513] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11149/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11149/checkm_input OceanDNA-b11149/checkm_result
[2023-03-19 00:30:41,920] [INFO] Task succeeded: CheckM
[2023-03-19 00:30:41,920] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.44%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 00:30:41,922] [INFO] ===== Completeness check finished =====
[2023-03-19 00:30:41,922] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:30:41,922] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11149/markers.fasta)
[2023-03-19 00:30:41,923] [INFO] Task started: Blastn
[2023-03-19 00:30:41,923] [INFO] Running command: blastn -query OceanDNA-b11149/markers.fasta -db /var/lib/cwl/stg9c71fd04-392f-4721-9876-c81435ce3e62/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11149/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:30:42,670] [INFO] Task succeeded: Blastn
[2023-03-19 00:30:42,671] [INFO] Selected 8 target genomes.
[2023-03-19 00:30:42,671] [INFO] Target genome list was writen to OceanDNA-b11149/target_genomes_gtdb.txt
[2023-03-19 00:30:42,681] [INFO] Task started: fastANI
[2023-03-19 00:30:42,681] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ad3324e-0132-49c8-8aa0-f4d4d59e7c95/OceanDNA-b11149.fa --refList OceanDNA-b11149/target_genomes_gtdb.txt --output OceanDNA-b11149/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:30:45,170] [INFO] Task succeeded: fastANI
[2023-03-19 00:30:45,175] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 00:30:45,175] [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_002862705.1	s__UBA7446 sp002862705	99.3863	324	370	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	99.06	98.27	0.87	0.83	14	conclusive
GCA_002313325.1	s__UBA7446 sp002313325	92.3035	222	370	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	99.90	99.90	0.92	0.92	2	-
GCA_009886265.1	s__UBA7446 sp009886265	90.8433	277	370	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862645.1	s__UBA7446 sp002862645	83.5425	259	370	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	95.15	95.15	0.79	0.79	2	-
GCA_002698745.1	s__UBA7446 sp002698745	83.4983	245	370	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002478685.1	s__UBA7446 sp002478685	77.5817	118	370	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	99.74	99.74	0.91	0.91	3	-
--------------------------------------------------------------------------------
[2023-03-19 00:30:45,175] [INFO] GTDB search result was written to OceanDNA-b11149/result_gtdb.tsv
[2023-03-19 00:30:45,176] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:30:45,176] [INFO] DFAST_QC result json was written to OceanDNA-b11149/dqc_result.json
[2023-03-19 00:30:45,176] [INFO] DFAST_QC completed!
[2023-03-19 00:30:45,176] [INFO] Total running time: 0h0m59s