[2024-01-24 11:34:36,994] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:36,996] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:36,996] [INFO] DQC Reference Directory: /var/lib/cwl/stg0fee3594-fb72-4c0d-a9a3-e950019a43ca/dqc_reference
[2024-01-24 11:34:39,641] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:39,642] [INFO] Task started: Prodigal
[2024-01-24 11:34:39,642] [INFO] Running command: gunzip -c /var/lib/cwl/stg8bd527d3-b0f2-4da0-918e-917f9bd59906/GCF_016464705.1_ASM1646470v1_genomic.fna.gz | prodigal -d GCF_016464705.1_ASM1646470v1_genomic.fna/cds.fna -a GCF_016464705.1_ASM1646470v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:34:59,706] [INFO] Task succeeded: Prodigal
[2024-01-24 11:34:59,707] [INFO] Task started: HMMsearch
[2024-01-24 11:34:59,707] [INFO] Running command: hmmsearch --tblout GCF_016464705.1_ASM1646470v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0fee3594-fb72-4c0d-a9a3-e950019a43ca/dqc_reference/reference_markers.hmm GCF_016464705.1_ASM1646470v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:00,112] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:00,113] [INFO] Found 6/6 markers.
[2024-01-24 11:35:00,167] [INFO] Query marker FASTA was written to GCF_016464705.1_ASM1646470v1_genomic.fna/markers.fasta
[2024-01-24 11:35:00,167] [INFO] Task started: Blastn
[2024-01-24 11:35:00,167] [INFO] Running command: blastn -query GCF_016464705.1_ASM1646470v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0fee3594-fb72-4c0d-a9a3-e950019a43ca/dqc_reference/reference_markers.fasta -out GCF_016464705.1_ASM1646470v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:01,527] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:01,530] [INFO] Selected 20 target genomes.
[2024-01-24 11:35:01,531] [INFO] Target genome list was writen to GCF_016464705.1_ASM1646470v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:01,538] [INFO] Task started: fastANI
[2024-01-24 11:35:01,539] [INFO] Running command: fastANI --query /var/lib/cwl/stg8bd527d3-b0f2-4da0-918e-917f9bd59906/GCF_016464705.1_ASM1646470v1_genomic.fna.gz --refList GCF_016464705.1_ASM1646470v1_genomic.fna/target_genomes.txt --output GCF_016464705.1_ASM1646470v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:34,910] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:34,911] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0fee3594-fb72-4c0d-a9a3-e950019a43ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:34,911] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0fee3594-fb72-4c0d-a9a3-e950019a43ca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:34,927] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:35:34,928] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:35:34,928] [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
Prauserella muralis	strain=DSM 45305	GCA_003202285.1	588067	588067	type	True	82.5134	1412	2149	95	below_threshold
Prauserella muralis	strain=DSM 45305	GCA_007993965.1	588067	588067	type	True	82.5012	1410	2149	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	81.3966	1173	2149	95	below_threshold
Amycolatopsis arida	strain=CGMCC 4.5579	GCA_900115565.1	587909	587909	type	True	81.0652	1066	2149	95	below_threshold
Amycolatopsis arida	strain=DSM 45648	GCA_004365925.1	587909	587909	type	True	81.0367	1070	2149	95	below_threshold
Amycolatopsis aidingensis	strain=YIM 96748	GCA_018885265.1	2842453	2842453	type	True	80.432	1082	2149	95	below_threshold
Amycolatopsis cihanbeyliensis	strain=DSM 45679	GCA_006715045.1	1128664	1128664	type	True	80.2756	1067	2149	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	80.2703	1046	2149	95	below_threshold
Amycolatopsis nigrescens	strain=CSC17Ta-90	GCA_000384315.1	381445	381445	type	True	80.2181	1127	2149	95	below_threshold
Amycolatopsis acidiphila	strain=KCTC 39523	GCA_021391495.1	715473	715473	type	True	80.1635	1038	2149	95	below_threshold
Amycolatopsis anabasis	strain=EGI 650086	GCA_009765355.1	1840409	1840409	type	True	80.0892	1126	2149	95	below_threshold
Amycolatopsis methanolica	strain=239	GCA_000739085.1	1814	1814	type	True	80.0832	1053	2149	95	below_threshold
Amycolatopsis bartoniae	strain=DSM 45807	GCA_007713755.1	941986	941986	type	True	79.9797	978	2149	95	below_threshold
Amycolatopsis methanolica	strain=239	GCA_000371885.1	1814	1814	type	True	79.9781	1062	2149	95	below_threshold
Amycolatopsis magusensis	strain=DSM 45510	GCA_017875555.1	882444	882444	type	True	79.977	1098	2149	95	below_threshold
Amycolatopsis bartoniae	strain=DSM 45807	GCA_014191255.1	941986	941986	type	True	79.9455	1010	2149	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	79.2191	1087	2149	95	below_threshold
Amycolatopsis lexingtonensis	strain=DSM 44653	GCA_014873755.1	218822	218822	type	True	79.2162	1113	2149	95	below_threshold
Amycolatopsis lexingtonensis	strain=NRRL B-24131	GCA_002156005.1	218822	218822	type	True	79.1332	1041	2149	95	below_threshold
Allokutzneria albata	strain=NRRL B-24461	GCA_000720955.1	211114	211114	type	True	77.9176	765	2149	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:34,929] [INFO] DFAST Taxonomy check result was written to GCF_016464705.1_ASM1646470v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:34,930] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:34,930] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:34,930] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0fee3594-fb72-4c0d-a9a3-e950019a43ca/dqc_reference/checkm_data
[2024-01-24 11:35:34,931] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:34,989] [INFO] Task started: CheckM
[2024-01-24 11:35:34,990] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016464705.1_ASM1646470v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016464705.1_ASM1646470v1_genomic.fna/checkm_input GCF_016464705.1_ASM1646470v1_genomic.fna/checkm_result
[2024-01-24 11:36:36,552] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:36,553] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:36,573] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:36,573] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:36,574] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016464705.1_ASM1646470v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:36,574] [INFO] Task started: Blastn
[2024-01-24 11:36:36,574] [INFO] Running command: blastn -query GCF_016464705.1_ASM1646470v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0fee3594-fb72-4c0d-a9a3-e950019a43ca/dqc_reference/reference_markers_gtdb.fasta -out GCF_016464705.1_ASM1646470v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:38,486] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:38,490] [INFO] Selected 15 target genomes.
[2024-01-24 11:36:38,490] [INFO] Target genome list was writen to GCF_016464705.1_ASM1646470v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:38,499] [INFO] Task started: fastANI
[2024-01-24 11:36:38,499] [INFO] Running command: fastANI --query /var/lib/cwl/stg8bd527d3-b0f2-4da0-918e-917f9bd59906/GCF_016464705.1_ASM1646470v1_genomic.fna.gz --refList GCF_016464705.1_ASM1646470v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016464705.1_ASM1646470v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:37:03,419] [INFO] Task succeeded: fastANI
[2024-01-24 11:37:03,431] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:37:03,432] [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_016464705.1	s__Saccharomonospora sp016464705	100.0	2145	2149	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003001955.1	s__Saccharomonospora shujinwangii	83.9225	1414	2149	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003202285.1	s__Saccharomonospora muralis	82.5704	1402	2149	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003202235.1	s__Saccharomonospora sp003202235	82.0137	1278	2149	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005146945.1	s__Saccharomonospora endophytica	81.964	1243	2149	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	99.14	99.02	0.90	0.90	3	-
GCF_900115565.1	s__Yuhushiella arida	81.0546	1068	2149	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Yuhushiella	95.0	100.00	100.00	0.99	0.99	2	-
GCF_018885265.1	s__Amycolatopsis_D sp018885265	80.441	1080	2149	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715045.1	s__Amycolatopsis_D cihanbeyliensis	80.2761	1067	2149	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000384315.1	s__Amycolatopsis nigrescens	80.23	1125	2149	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004214935.1	s__Amycolatopsis suaedae	80.1538	1060	2149	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765355.1	s__Amycolatopsis anabasis	80.0694	1130	2149	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003312875.1	s__Amycolatopsis albispora	80.0463	1112	2149	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002262875.1	s__Amycolatopsis antarctica	79.8675	903	2149	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873755.1	s__Amycolatopsis lexingtonensis	79.2413	1107	2149	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900103775.1	s__Allokutzneria albata	77.9386	759	2149	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Allokutzneria	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:37:03,433] [INFO] GTDB search result was written to GCF_016464705.1_ASM1646470v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:37:03,433] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:37:03,437] [INFO] DFAST_QC result json was written to GCF_016464705.1_ASM1646470v1_genomic.fna/dqc_result.json
[2024-01-24 11:37:03,438] [INFO] DFAST_QC completed!
[2024-01-24 11:37:03,438] [INFO] Total running time: 0h2m26s