[2024-01-24 13:57:57,430] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:57,434] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:57,434] [INFO] DQC Reference Directory: /var/lib/cwl/stg874fa083-7478-4a80-a071-5036c43c9c57/dqc_reference
[2024-01-24 13:57:58,715] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:58,716] [INFO] Task started: Prodigal
[2024-01-24 13:57:58,716] [INFO] Running command: gunzip -c /var/lib/cwl/stg72632fd1-5a16-42f7-89fe-e76723785f80/GCF_019492185.1_ASM1949218v1_genomic.fna.gz | prodigal -d GCF_019492185.1_ASM1949218v1_genomic.fna/cds.fna -a GCF_019492185.1_ASM1949218v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:38,112] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:38,113] [INFO] Task started: HMMsearch
[2024-01-24 13:58:38,113] [INFO] Running command: hmmsearch --tblout GCF_019492185.1_ASM1949218v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg874fa083-7478-4a80-a071-5036c43c9c57/dqc_reference/reference_markers.hmm GCF_019492185.1_ASM1949218v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:38,530] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:38,531] [INFO] Found 6/6 markers.
[2024-01-24 13:58:38,587] [INFO] Query marker FASTA was written to GCF_019492185.1_ASM1949218v1_genomic.fna/markers.fasta
[2024-01-24 13:58:38,587] [INFO] Task started: Blastn
[2024-01-24 13:58:38,587] [INFO] Running command: blastn -query GCF_019492185.1_ASM1949218v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg874fa083-7478-4a80-a071-5036c43c9c57/dqc_reference/reference_markers.fasta -out GCF_019492185.1_ASM1949218v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:39,213] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:39,215] [INFO] Selected 7 target genomes.
[2024-01-24 13:58:39,216] [INFO] Target genome list was writen to GCF_019492185.1_ASM1949218v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:39,243] [INFO] Task started: fastANI
[2024-01-24 13:58:39,243] [INFO] Running command: fastANI --query /var/lib/cwl/stg72632fd1-5a16-42f7-89fe-e76723785f80/GCF_019492185.1_ASM1949218v1_genomic.fna.gz --refList GCF_019492185.1_ASM1949218v1_genomic.fna/target_genomes.txt --output GCF_019492185.1_ASM1949218v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:50,534] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:50,535] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg874fa083-7478-4a80-a071-5036c43c9c57/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:50,535] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg874fa083-7478-4a80-a071-5036c43c9c57/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:50,546] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:50,546] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:50,547] [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
Chitinophaga rhizophila	strain=B61	GCA_019492185.1	2866212	2866212	type	True	100.0	2527	2527	95	conclusive
Chitinophaga pinensis	strain=DSM 2588	GCA_000024005.1	79329	79329	type	True	81.9564	1465	2527	95	below_threshold
Chitinophaga agri	strain=H33E-04	GCA_010093065.1	2703787	2703787	type	True	81.8076	1452	2527	95	below_threshold
Chitinophaga filiformis	strain=DSM 527	GCA_900102545.1	104663	104663	type	True	80.506	1109	2527	95	below_threshold
Chitinophaga ginsengisoli	strain=DSM 18107	GCA_003014595.1	363837	363837	type	True	80.4119	1102	2527	95	below_threshold
Chitinophaga tropicalis	strain=ysch24	GCA_009758205.1	2683588	2683588	type	True	79.2444	750	2527	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:50,548] [INFO] DFAST Taxonomy check result was written to GCF_019492185.1_ASM1949218v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:50,549] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:50,549] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:50,549] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg874fa083-7478-4a80-a071-5036c43c9c57/dqc_reference/checkm_data
[2024-01-24 13:58:50,551] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:50,618] [INFO] Task started: CheckM
[2024-01-24 13:58:50,618] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019492185.1_ASM1949218v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019492185.1_ASM1949218v1_genomic.fna/checkm_input GCF_019492185.1_ASM1949218v1_genomic.fna/checkm_result
[2024-01-24 14:00:41,947] [INFO] Task succeeded: CheckM
[2024-01-24 14:00:41,948] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:00:41,974] [INFO] ===== Completeness check finished =====
[2024-01-24 14:00:41,974] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:00:41,975] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019492185.1_ASM1949218v1_genomic.fna/markers.fasta)
[2024-01-24 14:00:41,975] [INFO] Task started: Blastn
[2024-01-24 14:00:41,975] [INFO] Running command: blastn -query GCF_019492185.1_ASM1949218v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg874fa083-7478-4a80-a071-5036c43c9c57/dqc_reference/reference_markers_gtdb.fasta -out GCF_019492185.1_ASM1949218v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:00:42,771] [INFO] Task succeeded: Blastn
[2024-01-24 14:00:42,777] [INFO] Selected 10 target genomes.
[2024-01-24 14:00:42,777] [INFO] Target genome list was writen to GCF_019492185.1_ASM1949218v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:00:42,845] [INFO] Task started: fastANI
[2024-01-24 14:00:42,846] [INFO] Running command: fastANI --query /var/lib/cwl/stg72632fd1-5a16-42f7-89fe-e76723785f80/GCF_019492185.1_ASM1949218v1_genomic.fna.gz --refList GCF_019492185.1_ASM1949218v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019492185.1_ASM1949218v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:59,645] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:59,660] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:00:59,661] [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
GCF_007896845.1	s__Chitinophaga pinensis_C	82.0936	1387	2527	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114995.1	s__Chitinophaga sp900114995	81.956	1463	2527	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024005.1	s__Chitinophaga pinensis	81.9521	1467	2527	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010093065.1	s__Chitinophaga agri	81.8237	1448	2527	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016467415.1	s__Chitinophaga sp016467415	80.5623	1079	2527	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003182155.1	s__Chitinophaga sp003182155	80.5415	1079	2527	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142925.1	s__Chitinophaga sp900142925	80.5326	1098	2527	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102545.1	s__Chitinophaga filiformis	80.5115	1108	2527	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003014595.1	s__Chitinophaga ginsengisoli	80.4067	1103	2527	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902168105.1	s__Chitinophaga sp902168105	80.2754	1085	2527	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Chitinophaga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:00:59,663] [INFO] GTDB search result was written to GCF_019492185.1_ASM1949218v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:59,663] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:59,666] [INFO] DFAST_QC result json was written to GCF_019492185.1_ASM1949218v1_genomic.fna/dqc_result.json
[2024-01-24 14:00:59,666] [INFO] DFAST_QC completed!
[2024-01-24 14:00:59,666] [INFO] Total running time: 0h3m2s