[2023-06-28 12:03:48,940] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:03:48,943] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:03:48,944] [INFO] DQC Reference Directory: /var/lib/cwl/stg1b965506-a01c-4e57-a517-aa7d271aeb9b/dqc_reference
[2023-06-28 12:03:50,302] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:03:50,303] [INFO] Task started: Prodigal
[2023-06-28 12:03:50,304] [INFO] Running command: gunzip -c /var/lib/cwl/stg482031dd-70cd-4599-a11b-23b6d74f67c9/GCA_017452265.1_ASM1745226v1_genomic.fna.gz | prodigal -d GCA_017452265.1_ASM1745226v1_genomic.fna/cds.fna -a GCA_017452265.1_ASM1745226v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:04:05,053] [INFO] Task succeeded: Prodigal
[2023-06-28 12:04:05,054] [INFO] Task started: HMMsearch
[2023-06-28 12:04:05,054] [INFO] Running command: hmmsearch --tblout GCA_017452265.1_ASM1745226v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1b965506-a01c-4e57-a517-aa7d271aeb9b/dqc_reference/reference_markers.hmm GCA_017452265.1_ASM1745226v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:04:05,332] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:04:05,334] [INFO] Found 6/6 markers.
[2023-06-28 12:04:05,363] [INFO] Query marker FASTA was written to GCA_017452265.1_ASM1745226v1_genomic.fna/markers.fasta
[2023-06-28 12:04:05,363] [INFO] Task started: Blastn
[2023-06-28 12:04:05,363] [INFO] Running command: blastn -query GCA_017452265.1_ASM1745226v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b965506-a01c-4e57-a517-aa7d271aeb9b/dqc_reference/reference_markers.fasta -out GCA_017452265.1_ASM1745226v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:04:06,008] [INFO] Task succeeded: Blastn
[2023-06-28 12:04:06,014] [INFO] Selected 29 target genomes.
[2023-06-28 12:04:06,015] [INFO] Target genome list was writen to GCA_017452265.1_ASM1745226v1_genomic.fna/target_genomes.txt
[2023-06-28 12:04:06,025] [INFO] Task started: fastANI
[2023-06-28 12:04:06,026] [INFO] Running command: fastANI --query /var/lib/cwl/stg482031dd-70cd-4599-a11b-23b6d74f67c9/GCA_017452265.1_ASM1745226v1_genomic.fna.gz --refList GCA_017452265.1_ASM1745226v1_genomic.fna/target_genomes.txt --output GCA_017452265.1_ASM1745226v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:04:24,383] [INFO] Task succeeded: fastANI
[2023-06-28 12:04:24,384] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1b965506-a01c-4e57-a517-aa7d271aeb9b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:04:24,384] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1b965506-a01c-4e57-a517-aa7d271aeb9b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:04:24,386] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:04:24,386] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 12:04:24,386] [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
--------------------------------------------------------------------------------
[2023-06-28 12:04:24,388] [INFO] DFAST Taxonomy check result was written to GCA_017452265.1_ASM1745226v1_genomic.fna/tc_result.tsv
[2023-06-28 12:04:24,389] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:04:24,389] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:04:24,389] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1b965506-a01c-4e57-a517-aa7d271aeb9b/dqc_reference/checkm_data
[2023-06-28 12:04:24,392] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:04:24,424] [INFO] Task started: CheckM
[2023-06-28 12:04:24,424] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017452265.1_ASM1745226v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017452265.1_ASM1745226v1_genomic.fna/checkm_input GCA_017452265.1_ASM1745226v1_genomic.fna/checkm_result
[2023-06-28 12:05:09,496] [INFO] Task succeeded: CheckM
[2023-06-28 12:05:09,498] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.69%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 12:05:09,525] [INFO] ===== Completeness check finished =====
[2023-06-28 12:05:09,525] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:05:09,526] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017452265.1_ASM1745226v1_genomic.fna/markers.fasta)
[2023-06-28 12:05:09,526] [INFO] Task started: Blastn
[2023-06-28 12:05:09,526] [INFO] Running command: blastn -query GCA_017452265.1_ASM1745226v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b965506-a01c-4e57-a517-aa7d271aeb9b/dqc_reference/reference_markers_gtdb.fasta -out GCA_017452265.1_ASM1745226v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:05:10,373] [INFO] Task succeeded: Blastn
[2023-06-28 12:05:10,378] [INFO] Selected 18 target genomes.
[2023-06-28 12:05:10,379] [INFO] Target genome list was writen to GCA_017452265.1_ASM1745226v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:05:10,389] [INFO] Task started: fastANI
[2023-06-28 12:05:10,389] [INFO] Running command: fastANI --query /var/lib/cwl/stg482031dd-70cd-4599-a11b-23b6d74f67c9/GCA_017452265.1_ASM1745226v1_genomic.fna.gz --refList GCA_017452265.1_ASM1745226v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017452265.1_ASM1745226v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:05:17,462] [INFO] Task succeeded: fastANI
[2023-06-28 12:05:17,479] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 12:05:17,480] [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_017452265.1	s__Cryptobacteroides sp017452265	100.0	821	829	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017937885.1	s__Cryptobacteroides sp017937885	79.4091	191	829	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017938925.1	s__Cryptobacteroides sp017938925	79.2697	260	829	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.18	96.33	0.77	0.70	3	-
GCA_017465225.1	s__Cryptobacteroides sp017465225	79.1938	241	829	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.02	96.60	0.67	0.61	4	-
GCA_017437125.1	s__Cryptobacteroides sp017437125	79.03	253	829	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017415715.1	s__Cryptobacteroides sp017415715	78.9639	256	829	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017502125.1	s__Cryptobacteroides sp017502125	78.9318	210	829	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017398335.1	s__Cryptobacteroides sp017398335	78.9226	152	829	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017626355.1	s__Cryptobacteroides sp017626355	78.8574	200	829	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017561265.1	s__Cryptobacteroides sp017561265	78.7481	162	829	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017461285.1	s__Cryptobacteroides sp017461285	78.7001	233	829	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017631875.1	s__Cryptobacteroides sp017631875	78.6672	206	829	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017555445.1	s__Cryptobacteroides sp017555445	78.6041	163	829	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015060325.1	s__Cryptobacteroides sp015060325	78.5843	195	829	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017549505.1	s__Cryptobacteroides sp017549505	78.4386	205	829	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017472115.1	s__Cryptobacteroides sp017472115	78.301	182	829	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017442315.1	s__Cryptobacteroides sp017442315	78.1101	142	829	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.71	98.71	0.80	0.80	2	-
GCA_017546275.1	s__Cryptobacteroides sp017546275	77.8537	137	829	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 12:05:17,482] [INFO] GTDB search result was written to GCA_017452265.1_ASM1745226v1_genomic.fna/result_gtdb.tsv
[2023-06-28 12:05:17,482] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:05:17,486] [INFO] DFAST_QC result json was written to GCA_017452265.1_ASM1745226v1_genomic.fna/dqc_result.json
[2023-06-28 12:05:17,487] [INFO] DFAST_QC completed!
[2023-06-28 12:05:17,487] [INFO] Total running time: 0h1m29s