[2023-03-14 13:39:23,944] [INFO] DFAST_QC pipeline started.
[2023-03-14 13:39:23,944] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 13:39:23,944] [INFO] DQC Reference Directory: /var/lib/cwl/stg39ef851a-018e-4c9a-aaec-37327ceff965/dqc_reference
[2023-03-14 13:39:25,035] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 13:39:25,036] [INFO] Task started: Prodigal
[2023-03-14 13:39:25,036] [INFO] Running command: cat /var/lib/cwl/stg015c055a-1663-42f6-b6ee-2dac483cfb4d/OceanDNA-b22121.fa | prodigal -d OceanDNA-b22121/cds.fna -a OceanDNA-b22121/protein.faa -g 11 -q > /dev/null
[2023-03-14 13:39:47,585] [INFO] Task succeeded: Prodigal
[2023-03-14 13:39:47,585] [INFO] Task started: HMMsearch
[2023-03-14 13:39:47,585] [INFO] Running command: hmmsearch --tblout OceanDNA-b22121/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg39ef851a-018e-4c9a-aaec-37327ceff965/dqc_reference/reference_markers.hmm OceanDNA-b22121/protein.faa > /dev/null
[2023-03-14 13:39:47,776] [INFO] Task succeeded: HMMsearch
[2023-03-14 13:39:47,777] [INFO] Found 6/6 markers.
[2023-03-14 13:39:47,793] [INFO] Query marker FASTA was written to OceanDNA-b22121/markers.fasta
[2023-03-14 13:39:47,795] [INFO] Task started: Blastn
[2023-03-14 13:39:47,795] [INFO] Running command: blastn -query OceanDNA-b22121/markers.fasta -db /var/lib/cwl/stg39ef851a-018e-4c9a-aaec-37327ceff965/dqc_reference/reference_markers.fasta -out OceanDNA-b22121/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:39:48,354] [INFO] Task succeeded: Blastn
[2023-03-14 13:39:48,355] [INFO] Selected 24 target genomes.
[2023-03-14 13:39:48,355] [INFO] Target genome list was writen to OceanDNA-b22121/target_genomes.txt
[2023-03-14 13:39:48,367] [INFO] Task started: fastANI
[2023-03-14 13:39:48,367] [INFO] Running command: fastANI --query /var/lib/cwl/stg015c055a-1663-42f6-b6ee-2dac483cfb4d/OceanDNA-b22121.fa --refList OceanDNA-b22121/target_genomes.txt --output OceanDNA-b22121/fastani_result.tsv --threads 1
[2023-03-14 13:40:09,809] [INFO] Task succeeded: fastANI
[2023-03-14 13:40:09,809] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg39ef851a-018e-4c9a-aaec-37327ceff965/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 13:40:09,809] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg39ef851a-018e-4c9a-aaec-37327ceff965/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 13:40:09,809] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 13:40:09,809] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 13:40:09,809] [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
--------------------------------------------------------------------------------
[2023-03-14 13:40:09,810] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22121/tc_result.tsv
[2023-03-14 13:40:09,810] [INFO] ===== Taxonomy check completed =====
[2023-03-14 13:40:09,810] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 13:40:09,810] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg39ef851a-018e-4c9a-aaec-37327ceff965/dqc_reference/checkm_data
[2023-03-14 13:40:09,813] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 13:40:09,817] [INFO] Task started: CheckM
[2023-03-14 13:40:09,817] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22121/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22121/checkm_input OceanDNA-b22121/checkm_result
[2023-03-14 13:40:55,937] [INFO] Task succeeded: CheckM
[2023-03-14 13:40:55,937] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 13:40:55,941] [INFO] ===== Completeness check finished =====
[2023-03-14 13:40:55,941] [INFO] ===== Start GTDB Search =====
[2023-03-14 13:40:55,941] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22121/markers.fasta)
[2023-03-14 13:40:55,943] [INFO] Task started: Blastn
[2023-03-14 13:40:55,943] [INFO] Running command: blastn -query OceanDNA-b22121/markers.fasta -db /var/lib/cwl/stg39ef851a-018e-4c9a-aaec-37327ceff965/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22121/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:40:56,888] [INFO] Task succeeded: Blastn
[2023-03-14 13:40:56,889] [INFO] Selected 7 target genomes.
[2023-03-14 13:40:56,889] [INFO] Target genome list was writen to OceanDNA-b22121/target_genomes_gtdb.txt
[2023-03-14 13:40:56,943] [INFO] Task started: fastANI
[2023-03-14 13:40:56,943] [INFO] Running command: fastANI --query /var/lib/cwl/stg015c055a-1663-42f6-b6ee-2dac483cfb4d/OceanDNA-b22121.fa --refList OceanDNA-b22121/target_genomes_gtdb.txt --output OceanDNA-b22121/fastani_result_gtdb.tsv --threads 1
[2023-03-14 13:41:03,823] [INFO] Task succeeded: fastANI
[2023-03-14 13:41:03,829] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 13:41:03,830] [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_005789005.1	s__SYAC01 sp005789005	90.0751	485	693	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__SYAC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903831295.1	s__SYAC01 sp903831295	89.4078	578	693	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__SYAC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903914045.1	s__SYAC01 sp903914045	86.5184	355	693	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__SYAC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009691785.1	s__SYAC01 sp009691785	86.3838	510	693	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__SYAC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903898755.1	s__SYAC01 sp903898755	85.8335	540	693	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__SYAC01	95.0	99.48	98.74	0.91	0.88	11	-
GCA_903938205.1	s__SYAC01 sp903938205	85.7635	382	693	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__SYAC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005787685.1	s__SYAC01 sp005787685	83.2243	493	693	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__SYAC01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 13:41:03,830] [INFO] GTDB search result was written to OceanDNA-b22121/result_gtdb.tsv
[2023-03-14 13:41:03,830] [INFO] ===== GTDB Search completed =====
[2023-03-14 13:41:03,831] [INFO] DFAST_QC result json was written to OceanDNA-b22121/dqc_result.json
[2023-03-14 13:41:03,832] [INFO] DFAST_QC completed!
[2023-03-14 13:41:03,832] [INFO] Total running time: 0h1m40s